sesameData

https://github.com/zwdzwd/sesamedata
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### Retrieve Probes by Gene or Promoter

Source: https://github.com/zwdzwd/sesamedata/blob/devel/man/sesameData_getProbesByGene.Rd

Examples demonstrating how to fetch probes for a specific gene and how to restrict the search to promoter regions.

```R
## download needed data
sesameDataCache(c("Mammal40.address", "genomeInfo.hg38"))

## get all probes overlapping with DNMT3A
probes <- sesameData_getProbesByGene(
    'DNMT3A', "Mammal40", upstream=500, downstream=500)

## get the promoter-associated probes
probes <- sesameData_getProbesByGene('DNMT3A', "Mammal40", promoter = TRUE)
```

--------------------------------

### Setup and Basic Probe Annotation

Source: https://github.com/zwdzwd/sesamedata/blob/devel/man/sesameData_annoProbes.Rd

Initializes the required data cache and demonstrates default gene annotation for specific probe IDs.

```R
library(GenomicRanges)
sesameDataCache(c(
    "genomeInfo.mm10", "MM285.address",
    "genomeInfo.hg38", "Mammal40.address"))

## Example 1: Basic usage - annotate with gene names (default)
## When regs=NULL, function defaults to gene annotation
probes <- c("cg14620903", "cg22464003")
anno <- sesameData_annoProbes(probes)
## Returns GRanges with gene_name column
```

--------------------------------

### Merge Transcripts to Genes

Source: https://github.com/zwdzwd/sesamedata/blob/devel/man/sesameData_getTxnGRanges.Rd

Example showing how to retrieve transcript data with the merge2gene parameter enabled.

```R
## merged to genes
sesameData_getTxnGRanges("mm10", merge2gene = TRUE)
```

--------------------------------

### Retrieve probes by genomic region in R

Source: https://github.com/zwdzwd/sesamedata/blob/devel/man/sesameData_getProbesByRegion.Rd

Examples demonstrating how to fetch probes using GRanges objects, specific chromosomes, or by excluding chromosomes.

```R
## download needed data
sesameDataCache(c("Mammal40.address", "genomeInfo.hg38"))

## get probes in a region
library(GenomicRanges)
probes = sesameData_getProbesByRegion(
    GRanges('chr5', IRanges(135313937, 135419936)), platform = 'Mammal40')

## get all probes on chromosome 5
probes = sesameData_getProbesByRegion(chrm = "chr5", platform = "Mammal40")

## get all probes on chromosome X
probes = sesameData_getProbesByRegion(chrm = 'chrX', platform = "Mammal40")

## get all probes on both chromosome X and Y
probes = sesameData_getProbesByRegion(
    chrm = c('chrX', 'chrY'), platform = "Mammal40")

## get all autosomal probes
probes = sesameData_getProbesByRegion(
    chrm_to_exclude = c("chrX", "chrY"), platform = "Mammal40")
```

--------------------------------

### Controlling Annotation Output

Source: https://github.com/zwdzwd/sesamedata/blob/devel/man/sesameData_annoProbes.Rd

Examples of managing how multiple overlapping features are handled, including collapsing, expanding, or selecting a single entry.

```R
## Example 5: Control annotation collapsing behavior
## collapse=TRUE (default): multiple annotations concatenated with separator
anno_collapsed <- sesameData_annoProbes(
    c("cg14620903","cg22464003"), genes, column="gene_name",
    collapse=TRUE, sep=";")
## Multiple overlapping genes listed as "GENE1;GENE2;GENE3"

## collapse=FALSE: each probe-feature overlap gets separate entry
anno_expanded <- sesameData_annoProbes(
    c("cg14620903","cg22464003"), genes, column="gene_name",
    collapse=FALSE)
## Probes with multiple overlaps appear multiple times

## Example 6: Choose only first annotation when multiple exist
anno_one <- sesameData_annoProbes(
    c("cg14620903","cg22464003"), genes, column="gene_name",
    chooseOne=TRUE)
## Each probe gets only the first overlapping gene
```

--------------------------------

### Retrieve and Filter Transcript GRanges

Source: https://github.com/zwdzwd/sesamedata/blob/devel/man/sesameData_getTxnGRanges.Rd

Examples demonstrating how to fetch transcript data for a specific genome and filter the resulting GRanges object.

```R
## all mm10 transcripts
txns <- sesameData_getTxnGRanges("mm10")

## verified protein-coding transcripts
txns[(txns$transcript_type == "protein_coding" & txns$level <= 2)]
```

--------------------------------

### Infer platform from probe IDs

Source: https://github.com/zwdzwd/sesamedata/blob/devel/man/inferPlatformFromProbeIDs.Rd

Demonstrates how to cache the probe ID signature and infer the platform from a vector of probe IDs.

```R
sesameDataCache("probeIDSignature")
inferPlatformFromProbeIDs(c("cg14620903","cg22464003"))
```

--------------------------------

### Initialize sesameData and cache resources

Source: https://github.com/zwdzwd/sesamedata/blob/devel/vignettes/sesameData.Rmd

Loads the required libraries and caches specific genome and platform data locally for subsequent use.

```r
library(sesameData)
library(GenomicRanges)
sesameDataCache(c("genomeInfo.mm10", "HM450.address"))
```

--------------------------------

### Check genome assembly for a platform

Source: https://github.com/zwdzwd/sesamedata/blob/devel/man/sesameData_check_genome.Rd

Verify the supported genome assembly for a specified platform. Passing NULL for the genome argument allows the function to return the default or supported assembly for the platform.

```R
sesameData_check_genome(NULL, "Mammal40")
```

--------------------------------

### sesameData_getManifestGRanges(platform, genome = NULL)

Source: https://github.com/zwdzwd/sesamedata/blob/devel/man/sesameData_getManifestGRanges.Rd

Retrieves the Infinium manifest as a GRanges object. Users can specify the platform and optionally the genome; if the genome is not provided, it will be inferred.

```APIDOC
## sesameData_getManifestGRanges

### Description
Retrieves the Infinium manifest as a GRanges object for a given platform. Note that some unaligned probes are not included in the returned object.

### Signature
`sesameData_getManifestGRanges(platform, genome = NULL)`

### Parameters
- **platform** (string) - Required - The Infinium platform (e.g., "Mammal40", "MM285", "EPIC", "HM450").
- **genome** (string) - Optional - The genome build (e.g., "hg38", "mm10"). If not provided, the function will attempt to infer it.

### Returns
- **GRanges** - A GRanges object containing the manifest data.

### Example
```r
res <- sesameData_getManifestGRanges("Mammal40")
```
```

--------------------------------

### Display Session Information

Source: https://github.com/zwdzwd/sesamedata/blob/devel/vignettes/sesameData.Rmd

Prints the current R session details.

```r
sessionInfo()
```

--------------------------------

### List Available Data

Source: https://github.com/zwdzwd/sesamedata/blob/devel/vignettes/sesameData.Rmd

Displays the titles of all datasets available in the package.

```r
head(sesameDataList())
```

--------------------------------

### build_GENCODE_gtf(x)

Source: https://github.com/zwdzwd/sesamedata/blob/devel/man/build_GENCODE_gtf.Rd

Constructs a GRangesList object from a GENCODE GTF file located at the specified FTP URL.

```APIDOC
## build_GENCODE_gtf(x)

### Description
Builds a GRangesList object by downloading and parsing a GENCODE GTF file from the provided URL.

### Parameters
- **x** (character) - Required - The GENCODE FTP URL pointing to the GTF file.

### Returns
- **GRangesList** - A GRangesList object containing the parsed genomic features.
```

--------------------------------

### inferPlatformFromProbeIDs(Probe_IDs, silent = FALSE)

Source: https://github.com/zwdzwd/sesamedata/blob/devel/man/inferPlatformFromProbeIDs.Rd

Infers the platform code based on a provided list of probe IDs.

```APIDOC
## inferPlatformFromProbeIDs

### Description
Infers the platform code from a given set of probe IDs.

### Usage
`inferPlatformFromProbeIDs(Probe_IDs, silent = FALSE)`

### Arguments
- **Probe_IDs** (vector) - A vector of probe IDs to analyze.
- **silent** (logical) - If TRUE, suppresses status messages. Defaults to FALSE.

### Returns
- **platform code** (string) - The inferred platform code.

### Example
```R
inferPlatformFromProbeIDs(c("cg14620903","cg22464003"))
```
```

--------------------------------

### sesameDataGet_checkEnv(title)

Source: https://github.com/zwdzwd/sesamedata/blob/devel/man/sesameDataGet_checkEnv.Rd

Checks whether the provided title exists in the cacheEnv and retrieves the associated data.

```APIDOC
## sesameDataGet_checkEnv

### Description
Check whether the title exists in cacheEnv.

### Usage
`sesameDataGet_checkEnv(title)`

### Arguments
- **title** (string) - The title to check in the cache environment.

### Returns
- **value** (any) - The data associated with the title, or NULL if the title does not exist.
```

--------------------------------

### sesameData_check_genome(genome, platform)

Source: https://github.com/zwdzwd/sesamedata/blob/devel/man/sesameData_check_genome.Rd

Checks if a specified genome assembly is supported by the provided platform. Returns the genome as a string.

```APIDOC
## sesameData_check_genome

### Description
Finds the genome assembly version(s) supported for a specific platform.

### Usage
`sesameData_check_genome(genome, platform)`

### Arguments
- **genome** (string) - The genome assembly version (e.g., "mm10", "hg38") or NULL.
- **platform** (string) - The platform identifier (e.g., "HM27", "HM450", "EPIC", "EPICv2", "MSA").

### Returns
- **genome** (string) - The validated genome assembly version.

### Example
```R
sesameData_check_genome(NULL, "Mammal40")
```
```

--------------------------------

### Verify platform code

Source: https://github.com/zwdzwd/sesamedata/blob/devel/man/sesameData_check_platform.Rd

Validates a specific platform string. Note that custom platforms will trigger an error.

```R
sesameData_check_platform("HM450")
```

--------------------------------

### sesameData_check_platform(platform = NULL, probes = NULL, silent = TRUE)

Source: https://github.com/zwdzwd/sesamedata/blob/devel/man/sesameData_check_platform.Rd

Checks or guesses the platform code. Note that custom platforms may lead to errors.

```APIDOC
## sesameData_check_platform

### Description
Validates the platform code or attempts to guess it based on provided probes. Custom platforms will trigger an error.

### Signature
`sesameData_check_platform(platform = NULL, probes = NULL, silent = TRUE)`

### Parameters
- **platform** (string) - Optional - The input platform string.
- **probes** (vector) - Optional - Probes used to infer the platform.
- **silent** (boolean) - Optional - If TRUE, suppresses informational messages.

### Returns
- **platform code** (string) - The validated or inferred platform code.

### Example
```R
sesameData_check_platform("HM450")
```
```

--------------------------------

### Querying sesameData via ExperimentHub

Source: https://github.com/zwdzwd/sesamedata/blob/devel/man/df_master.Rd

Retrieve and list sesameData objects from ExperimentHub.

```R
library(ExperimentHub)
eh <- query(ExperimentHub(localHub=FALSE), c("sesameData", "v1.13.1"))
data.frame(name=eh$title, eh=names(eh))
```

--------------------------------

### Annotating with Custom Genomic Regions

Source: https://github.com/zwdzwd/sesamedata/blob/devel/man/sesameData_annoProbes.Rd

Demonstrates how to provide custom GRanges objects for annotation.

```R
## Example 7: Annotate with custom genomic regions
custom_regs <- GRanges(
    seqnames = c("chr5", "chr5"),
    ranges = IRanges(start = c(10000, 135350870),
                     end = c(135350866, 145369531)),
    feature_type = c("enhancer", "silencer"))
anno_custom <- sesameData_annoProbes(
    c("cg14620903","cg22464003"), custom_regs,
    column="feature_type", genome="hg38")
```

--------------------------------

### Cache Data Locally

Source: https://github.com/zwdzwd/sesamedata/blob/devel/vignettes/sesameData.Rmd

Downloads and caches all necessary data to the local disk to remove internet dependency.

```r
sesameDataCache()
```

--------------------------------

### Convert transcript GRanges to gene GRanges

Source: https://github.com/zwdzwd/sesamedata/blob/devel/man/sesameData_txnToGeneGRanges.Rd

Demonstrates the conversion of transcript-level GRanges to gene-level GRanges using the mm10 genome build.

```R
txns <- sesameData_getTxnGRanges("mm10")
genes <- sesameData_txnToGeneGRanges(txns)
```

--------------------------------

### sesameData_getGenomeInfo(genome)

Source: https://github.com/zwdzwd/sesamedata/blob/devel/man/sesameData_getGenomeInfo.Rd

Retrieves a list of genome info files for a given genome assembly.

```APIDOC
## sesameData_getGenomeInfo

### Description
Retrieves a list of genome info files for a specified genome assembly.

### Usage
`sesameData_getGenomeInfo(genome)`

### Arguments
- **genome** (string/object) - Required - The genome assembly identifier (e.g., "hg38", "mm10") or a GRanges object containing genome metadata.

### Returns
- **list** - A list of genome info files.

### Example
```R
res <- sesameData_getGenomeInfo("hg38")
```
```

--------------------------------

### Retrieve Infinium Manifest GRanges

Source: https://github.com/zwdzwd/sesamedata/blob/devel/man/sesameData_getManifestGRanges.Rd

Caches the platform address data and retrieves the corresponding GRanges object.

```R
sesameDataCache("Mammal40.address")
res <- sesameData_getManifestGRanges("Mammal40")
```

--------------------------------

### Load GenomicRanges

Source: https://github.com/zwdzwd/sesamedata/blob/devel/vignettes/sesameData.Rmd

Load the GenomicRanges library for handling genomic data structures.

```r
library(GenomicRanges)
```

--------------------------------

### Annotating with Specific Genomic Regions

Source: https://github.com/zwdzwd/sesamedata/blob/devel/man/sesameData_annoProbes.Rd

Demonstrates annotating mouse probes specifically against promoter regions.

```R
## Example 2: Annotate mouse probes with promoter regions
regs <- sesameData_getTxnGRanges("mm10")
Probe_IDs <- names(sesameData_getManifestGRanges("MM285"))[1:100]
anno <- sesameData_annoProbes(Probe_IDs, promoters(regs), column="gene_name")
## Probes overlapping promoters are annotated with gene names
```

--------------------------------

### sesameDataGet_resetEnv()

Source: https://github.com/zwdzwd/sesamedata/blob/devel/man/sesameDataGet_resetEnv.Rd

Clears the in-memory cache environment to free memory. Subsequent calls to sesameDataGet will reload data from disk.

```APIDOC
## sesameDataGet_resetEnv()

### Description
Clears the in-memory cache environment (sesameData:::cacheEnv) to free memory. This forces sesameDataGet to retrieve data from disk again rather than using the cached version.

### Usage
`sesameDataGet_resetEnv()`

### Returns
- **gc() output** (list) - The result of the garbage collection process.
```

--------------------------------

### Retrieve Manifest GRanges

Source: https://github.com/zwdzwd/sesamedata/blob/devel/vignettes/sesameData.Rmd

Fetches the GRanges object for a specific array platform.

```r
gr <- sesameData_getManifestGRanges("HM450")
length(gr)
```

--------------------------------

### Retrieve Specific Data Object

Source: https://github.com/zwdzwd/sesamedata/blob/devel/vignettes/sesameData.Rmd

Loads a specific data object into memory using its title.

```r
HM27.address <- sesameDataGet('HM27.address')
```

--------------------------------

### sesameData_getProbesByRegion(regs, chrm = NULL, beg = 1, end = -1, platform = NULL, chrm_to_exclude = NULL, genome = NULL)

Source: https://github.com/zwdzwd/sesamedata/blob/devel/man/sesameData_getProbesByRegion.Rd

Retrieves probes based on genomic coordinates or chromosome specifications.

```APIDOC
## sesameData_getProbesByRegion

### Description
The function takes a genomic coordinate or chromosome identifier and outputs a vector of probes on the specified platform that fall within the given genomic region.

### Parameters
- **regs** (GRanges) - Optional - Genomic ranges to query.
- **chrm** (character) - Optional - Chromosome identifier; if provided, regs are ignored.
- **beg** (numeric) - Optional - Start position, defaults to 1.
- **end** (numeric) - Optional - End position, defaults to chromosome end if -1.
- **platform** (character) - Optional - The platform identifier (e.g., EPICv2, EPIC, HM450).
- **chrm_to_exclude** (character) - Optional - Chromosome(s) to exclude from the results.
- **genome** (character) - Optional - Genome build (e.g., hg38, mm10). Inferred if not provided.

### Returns
- **GRanges** - A GRanges object containing the selected probes.
```

--------------------------------

### Resetting the sesameData cache

Source: https://github.com/zwdzwd/sesamedata/blob/devel/man/sesameDataGet_resetEnv.Rd

Clears the in-memory cache environment to free memory and force data re-retrieval from disk.

```R
sesameDataGet_resetEnv()
```

--------------------------------

### Retrieve Genome Information

Source: https://github.com/zwdzwd/sesamedata/blob/devel/man/sesameData_getGenomeInfo.Rd

Caches and retrieves genome information for a specified assembly such as hg38.

```R
sesameDataCache("genomeInfo.hg38")
res <- sesameData_getGenomeInfo("hg38")
```

--------------------------------

### List SeSAMe data with filter

Source: https://github.com/zwdzwd/sesamedata/blob/devel/man/sesameDataList.Rd

Retrieves a list of SeSAMe data objects that match the specified keyword.

```R
sesameDataList("KYCG")
```

--------------------------------

### sesameData_getProbesByGene(gene_name = NULL, platform = NULL, promoter = FALSE, upstream = 1500, downstream = 1500, genome = NULL)

Source: https://github.com/zwdzwd/sesamedata/blob/devel/man/sesameData_getProbesByGene.Rd

Retrieves probes mapped to a gene or promoter region. All transcripts for the gene are considered based on the UCSC RefGene database.

```APIDOC
## sesameData_getProbesByGene

### Description
Get probes mapped to a gene. All transcripts for the gene are considered. The function takes a gene name as appears in UCSC RefGene database. The platform and reference genome build can be changed with `platform` and `genome` options.

### Signature
`sesameData_getProbesByGene(gene_name = NULL, platform = NULL, promoter = FALSE, upstream = 1500, downstream = 1500, genome = NULL)`

### Parameters
- **gene_name** (string) - Optional - Gene name, if NULL return all genes.
- **platform** (string) - Optional - EPIC or HM450.
- **promoter** (boolean) - Optional - If TRUE, use TSS instead of the whole gene.
- **upstream** (numeric) - Optional - Number of bases to expand upstream of target gene.
- **downstream** (numeric) - Optional - Number of bases to expand downstream of target gene.
- **genome** (string) - Optional - hg38 or hg19.

### Returns
- **GRanges** - A GRanges object containing probes that fall into the given gene.

### Example
```R
probes <- sesameData_getProbesByGene('DNMT3A', "Mammal40", upstream=500, downstream=500)
```
```

--------------------------------

### Annotate Probes with Genomic Features

Source: https://github.com/zwdzwd/sesamedata/blob/devel/vignettes/sesameData.Rmd

Annotate probe IDs using genomic features stored in GRanges objects.

```r
input_probes <- names(sesameData_getManifestGRanges("Mammal40"))[1:500]

## annotate for promoter
regs <- promoters(sesameData_getTxnGRanges("hg38"))
sesameData_annoProbes(input_probes, regs, column = "gene_name")

## annotate for gene association
regs <- sesameData_getTxnGRanges("hg38", merge2gene = TRUE)
sesameData_annoProbes(input_probes, regs, column = "gene_name")

## get genes associated with probes
regs <- sesameData_getTxnGRanges("hg38", merge2gene = TRUE)
sesameData_annoProbes(input_probes, regs, return_ov_features=TRUE)

## get genes associated with probes extending 10kb
input_probes <- c("cg14620903","cg22464003")
sesameData_annoProbes(input_probes, regs+10000, column = "gene_name")
```

--------------------------------

### sesameData_annoProbes(Probe_IDs, regs = NULL, collapse = TRUE, chooseOne = FALSE, column = NULL, sep = ",", return_ov_probes = FALSE, return_ov_features = FALSE, out_name = NULL, platform = NULL, genome = NULL, silent = FALSE)

Source: https://github.com/zwdzwd/sesamedata/blob/devel/man/sesameData_annoProbes.Rd

Annotates probes based on genomic coordinate overlaps with provided genomic regions (GRanges).

```APIDOC
## Function: sesameData_annoProbes

### Description
Annotates probes based on genomic coordinate overlaps with provided genomic regions (GRanges). Columns in the manifests will be added to the annotation. If a probe has no overlap with the provided regions, it will be included in the results with NA.

### Parameters
- **Probe_IDs** (character vector) - Required - A character vector of probe IDs to annotate.
- **regs** (GRanges) - Optional - A GenomicRanges::GRanges object against which probes will be annotated. Defaults to genes if not provided.
- **collapse** (logical) - Optional - Whether to collapse multiple overlapping regions into one entry. Default is TRUE.
- **chooseOne** (logical) - Optional - If TRUE, chooses an arbitrary single annotation if multiple exist. Default is FALSE.
- **column** (character) - Optional - The column in 'regs' to use for annotation. If not given, returns all overlapping probes.
- **sep** (character) - Optional - The delimiter used for collapsing multiple annotations. Default is ",".
- **return_ov_probes** (logical) - Optional - If TRUE, returns overlapping probes in a GRanges object.
- **return_ov_features** (logical) - Optional - If TRUE, returns overlapping features in a GRanges object.
- **out_name** (character) - Optional - The column header for the annotation. Uses 'column' if not specified.
- **platform** (character) - Optional - The platform (e.g., EPIC, MM285). Inferred from Probe_IDs if not provided.
- **genome** (character) - Optional - The genome build (e.g., hg38, mm10). Inferred if not provided.
- **silent** (logical) - Optional - If TRUE, suppresses messages.

### Returns
- **GRanges** - A GRanges object containing the annotated columns.
```

--------------------------------

### extend(gr, upstream = 0, downstream = 0)

Source: https://github.com/zwdzwd/sesamedata/blob/devel/man/extend.Rd

Extends a GRanges object by a specified number of base pairs in the upstream and downstream directions.

```APIDOC
## extend(gr, upstream = 0, downstream = 0)

### Description
Extends a GenomicRanges::GRanges object by a specified distance in the upstream and downstream directions.

### Parameters
- **gr** (GenomicRanges::GRanges) - Required - The input GRanges object to be extended.
- **upstream** (numeric) - Optional - The distance to expand the range in the upstream direction. Defaults to 0.
- **downstream** (numeric) - Optional - The distance to expand the range in the downstream direction. Defaults to 0.

### Returns
- **GRanges** - A new GenomicRanges::GRanges object with the extended coordinates.
```

--------------------------------

### sesameDataGet(title, verbose = FALSE)

Source: https://github.com/zwdzwd/sesamedata/blob/devel/man/sesameDataGet.Rd

Retrieves a SeSAMe data object based on the provided title.

```APIDOC
## sesameDataGet

### Description
Retrieves a SeSAMe data object by its title. This function is used to load specific datasets into the R environment.

### Signature
`sesameDataGet(title, verbose = FALSE)`

### Parameters
- **title** (string) - Required - The title of the data object to retrieve.
- **verbose** (boolean) - Optional - Whether to output ExperimentHub messages. Defaults to FALSE.

### Returns
- **data object** - The requested data object.

### Example
```R
EPIC.1.SigDF <- sesameDataGet('EPIC.1.SigDF')
```
```

--------------------------------

### Check for existence of data titles

Source: https://github.com/zwdzwd/sesamedata/blob/devel/man/sesameDataHas.Rd

Verify if specific data titles are present in the sesameData collection.

```R
sesameDataHas(c("EPIC.address","EPIC.address.Nonexist"))
```

--------------------------------

### sesameDataCacheAll(data_titles = NULL)

Source: https://github.com/zwdzwd/sesamedata/blob/devel/man/sesameDataCacheAll.Rd

Caches all SeSAMe data or a specified subset of data.

```APIDOC
## sesameDataCacheAll

### Description
Cache all SeSAMe data. If specific data titles are provided, only those will be cached; otherwise, the function caches all available data.

### Usage
`sesameDataCacheAll(data_titles = NULL)`

### Parameters
- **data_titles** (character vector) - Optional - The specific data titles to cache. If not provided, all data is cached.

### Returns
- **TRUE** (logical) - Returns TRUE upon successful completion.

### Example
```r
sesameDataCacheAll()
```
```

--------------------------------

### Returning Overlapping Features or Probes

Source: https://github.com/zwdzwd/sesamedata/blob/devel/man/sesameData_annoProbes.Rd

Shows how to return the overlapping genomic features or filter for probes that overlap with specific features.

```R
## Example 3: Get features that overlap with probes
## return_ov_features=TRUE returns the overlapping genomic features
genes <- sesameData_getTxnGRanges("hg38", merge2gene = TRUE)
ov_genes <- sesameData_annoProbes(
    c("cg14620903","cg22464003"), genes, return_ov_features=TRUE)
## Returns GRanges of genes overlapping the probes

## Example 4: Get probes that overlap with features
## return_ov_probes=TRUE returns only overlapping probes
ov_probes <- sesameData_annoProbes(
    c("cg14620903","cg22464003"), genes, return_ov_probes=TRUE)
## Returns GRanges of probes that overlap genes
```

--------------------------------

### sesameDataCache(data_titles = NULL)

Source: https://github.com/zwdzwd/sesamedata/blob/devel/man/sesameDataCache.Rd

Caches SeSAMe data. If data_titles is not specified, all data is cached.

```APIDOC
## sesameDataCache

### Description
Cache SeSAMe data locally for faster access.

### Usage
`sesameDataCache(data_titles = NULL)`

### Arguments
- **data_titles** (character) - Optional - The specific data titles to cache. If not provided, all available data will be cached.

### Returns
- **TRUE** (logical) - Returns TRUE upon successful completion.

### Example
```R
sesameDataCache("genomeInfo.hg38")
```
```

--------------------------------

### sesameData_getTxnGRanges(genome = NULL, grl = NULL, merge2gene = FALSE)

Source: https://github.com/zwdzwd/sesamedata/blob/devel/man/sesameData_getTxnGRanges.Rd

Converts a GRangesList object to transcript GRanges. Users can specify the genome, provide an optional GRangesList, and choose whether to merge transcripts to genes.

```APIDOC
## sesameData_getTxnGRanges

### Description
Converts a GRangesList object to transcript GRanges.

### Parameters
- **genome** (string) - Optional - The genome assembly (e.g., "hg38", "mm10").
- **grl** (GRangesList) - Optional - A GRangesList object to be converted.
- **merge2gene** (boolean) - Optional - If TRUE, merges transcripts to genes.

### Returns
- **GRanges** - A GRanges object containing the transcript information.

### Example
```r
# Retrieve all mm10 transcripts
txns <- sesameData_getTxnGRanges("mm10")

# Merge transcripts to genes
sesameData_getTxnGRanges("mm10", merge2gene = TRUE)
```
```

--------------------------------

### Retrieve SeSAMe data

Source: https://github.com/zwdzwd/sesamedata/blob/devel/man/sesameDataGet.Rd

Caches the specified data object and then retrieves it into the workspace.

```R
sesameDataCache("EPIC.1.SigDF")
EPIC.1.SigDF <- sesameDataGet('EPIC.1.SigDF')
```

--------------------------------

### sesameDataList(filter = NULL, full = FALSE)

Source: https://github.com/zwdzwd/sesamedata/blob/devel/man/sesameDataList.Rd

Lists all available SeSAMe data titles, with optional filtering and column display settings.

```APIDOC
## sesameDataList

### Description
Lists all available SeSAMe data titles. Users can optionally filter the results by a keyword or choose to display all columns.

### Usage
`sesameDataList(filter = NULL, full = FALSE)`

### Parameters
- **filter** (character) - Optional - A keyword used to filter the data titles.
- **full** (logical) - Optional - If set to TRUE, displays all columns in the output.

### Returns
- Returns a list or vector of titles from SeSAMe Data.

### Example
```R
sesameDataList("KYCG")
```
```

--------------------------------

### sesameDataHas(data_titles)

Source: https://github.com/zwdzwd/sesamedata/blob/devel/man/sesameDataHas.Rd

Checks if the provided data titles exist in the sesameData repository.

```APIDOC
## sesameDataHas

### Description
Checks whether specific data titles are available in the sesameData repository.

### Signature
`sesameDataHas(data_titles)`

### Parameters
- **data_titles** (character vector) - Required - A vector of data titles to check for existence.

### Returns
- **boolean vector** - A logical vector of the same length as `data_titles`, where TRUE indicates the data exists and FALSE indicates it does not.

### Example
```r
sesameDataHas(c("EPIC.address", "EPIC.address.Nonexist"))
```
```

--------------------------------

### Query Probes by Region or Gene

Source: https://github.com/zwdzwd/sesamedata/blob/devel/vignettes/sesameData.Rmd

Retrieve probe information based on specific genomic regions or gene associations.

```r
## probes in a region
sesameData_getProbesByRegion(GRanges('chr5',
    IRanges(135313937, 135419936)), platform = 'Mammal40')
## get chrX probes
sesameData_getProbesByRegion(chrm = 'chrX', platform = "Mammal40")
## get autosomal probes
sesameData_getProbesByRegion(
    chrm_to_exclude = c("chrX", "chrY"), platform = "Mammal40")
## get DNMT3A probes
sesameData_getProbesByGene('DNMT3A', "Mammal40", upstream=500)
## get DNMT3A promoter probes
sesameData_getProbesByGene('DNMT3A', "Mammal40", promoter = TRUE)
## get all promoter probes
sesameData_getProbesByGene(NULL, "Mammal40", promoter = TRUE)
```

--------------------------------

### Cache specific SeSAMe data

Source: https://github.com/zwdzwd/sesamedata/blob/devel/man/sesameDataCache.Rd

Caches the specified data title to the local environment.

```R
sesameDataCache("genomeInfo.hg38")
```

--------------------------------

### sesameData_txnToGeneGRanges(txns)

Source: https://github.com/zwdzwd/sesamedata/blob/devel/man/sesameData_txnToGeneGRanges.Rd

Converts a GRanges object containing transcript information into a GRanges object containing gene information.

```APIDOC
## sesameData_txnToGeneGRanges

### Description
Converts transcript GRanges to gene GRanges.

### Parameters
- **txns** (GRanges) - Required - A GRanges object representing transcripts.

### Returns
- **GRanges** - A GRanges object representing genes.

### Example
```R
txns <- sesameData_getTxnGRanges("mm10")
genes <- sesameData_txnToGeneGRanges(txns)
```
```

--------------------------------

### Retrieve Transcript GRanges

Source: https://github.com/zwdzwd/sesamedata/blob/devel/vignettes/sesameData.Rmd

Retrieve transcript-centric GRanges objects or collapse isoforms to gene level.

```r
sesameData_getTxnGRanges("mm10")
```

```r
sesameData_getTxnGRanges("mm10", merge2gene=TRUE)
```
Tokens:
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