### Install Sequenza R Package

Source: https://github.com/sztup/scarhrd/blob/master/README.md

Installs the latest version of the Sequenza R package from Bitbucket. Ensure R and devtools are installed.

```r
library(devtools)
install_bitbucket('sequenza_tools/sequenza')
```

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

### Sequenza Workflow Example

Source: https://github.com/sztup/scarhrd/blob/master/README.md

Example command for using Sequenza utilities to call allele specific copy number profile from BAM files. This step precedes scarHRD analysis.

```bash
sequenza-utils bam2seqz -gc /reference/GRCh38.gc50Base.txt.gz --fasta /reference/GRCh38.d1.vd1.fa -n /data/normal.bam --tumor /data/tumor.bam -C chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chr23 chr24 chrX | sequenza-utils seqz_binning -w 50 -s - | gzip > /results/tumor_small.seqz.gz
```

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

### Install scarHRD R Package

Source: https://github.com/sztup/scarhrd/blob/master/README.md

Installs the scarHRD R package from GitHub using devtools. Set build_vignettes to TRUE to include vignettes.

```r
library(devtools)
install_github('sztup/scarHRD',build_vignettes = TRUE)
```

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

### Install copynumber R Package for GRCh38

Source: https://github.com/sztup/scarhrd/blob/master/README.md

Installs a modified version of the copynumber R package from GitHub, necessary for running scarHRD on GRCh38.

```r
library(devtools)
install_github('aroneklund/copynumber')
```

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

### Read Sequenza Input File

Source: https://github.com/sztup/scarhrd/blob/master/scarHRD.md

Reads a Sequenza-formatted segmentation file into an R data frame. This is an example of preparing input data for scarHRD.

```r
example1<-system.file("extdata", "test1.small.seqz.gz", package = "scarHRD")
a<-read.table(example1, header=T)
head(a)
```

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

### Read Simplified Input File

Source: https://github.com/sztup/scarhrd/blob/master/scarHRD.md

Reads a simplified segmentation file into an R data frame. This example demonstrates handling a different input format for scarHRD.

```r
example2<-system.file("extdata", "test1.small.seqz.gz", package = "scarHRD")
a<-read.table(example2, header=T)
head(a)
```

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

### Run scarHRD on Mouse Genomes

Source: https://github.com/sztup/scarhrd/blob/master/scarHRD.md

Demonstrates how to specify a mouse reference genome for scarHRD analysis. Note the limitations in evaluating HRD scores for mouse genomes due to chromosomal structure and isogenic models.

```R
scarHRD(referrence="mouse")
```

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

### Calculate HRD Score from Text File

Source: https://github.com/sztup/scarhrd/blob/master/scarHRD.html

Calculates the HRD score using a .txt file. Ensure the 'grch38' reference genome is specified and seqz is set to FALSE.

```R
scar_score("/examples/test2.txt",reference = "grch38", seqz=FALSE)
```

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

### Read and Display Data Table

Source: https://github.com/sztup/scarhrd/blob/master/README.md

Reads a data table from a specified file path and displays the first few rows. This is useful for initial data inspection.

```r
a<-read.table("/examples/test2.txt", header=T)
head(a)
```

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

### Read scarHRD Input File

Source: https://github.com/sztup/scarhrd/blob/master/README.md

Reads a gzipped Sequenza segmentation file into an R data frame. This file serves as input for the scarHRD function.

```r
a<-read.table("/examples/test1.small.seqz.gz", header=T)
head(a)
```

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

### Calculate HRD Score from Seqz File

Source: https://github.com/sztup/scarhrd/blob/master/scarHRD.html

Calculates the HRD score using a .seqz.gz file. Ensure the 'grch38' reference genome is specified.

```R
scar_score("/examples/test1.small.seqz.gz",reference = "grch38", seqz=TRUE)
```

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

### Calculate scarHRD scores with different file types

Source: https://github.com/sztup/scarhrd/blob/master/scarHRD.md

Use scar_score to calculate HRD-LOH scores. Specify seqz=TRUE for .small.seqz.gz files and seqz=FALSE for .txt files. Ensure the reference genome is correctly set.

```r
scar_score("/examples/test1.small.seqz.gz",reference = "grch38", seqz=TRUE)
scar_score("/examples/test2.txt",reference = "grch38", seqz=FALSE)
```

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

### Calculate HRD Score from Text File

Source: https://github.com/sztup/scarhrd/blob/master/README.md

Calculates the scarHRD score using a plain text file. Set seqz to FALSE for non-seqz formatted files. This function determines HRD-LOH, LST, and TAI scores.

```r
scar_score("F:/Documents/scarHRD/examples/test2.txt",reference = "grch38", seqz=FALSE)
```

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

### Calculate HRD Score from Seqz File

Source: https://github.com/sztup/scarhrd/blob/master/README.md

Calculates the scarHRD score using a .seqz.gz file. Ensure the correct reference genome is specified. This function preprocesses the data and determines HRD, LST, and TAI scores.

```r
library("scarHRD")
scar_score("F:/Documents/scarHRD/examples/test1.small.seqz.gz",reference = "grch38", seqz=TRUE)
```

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