SeqArray

https://github.com/zhengxwen/seqarray
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SeqArray provides data management of large-scale whole-genome sequence variant calls, storing...
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### Install from Source Code

Source: https://github.com/zhengxwen/seqarray/blob/master/README.md

Download and install the package source files using wget or curl commands followed by R CMD INSTALL.

```sh
wget --no-check-certificate https://github.com/zhengxwen/gdsfmt/tarball/master -O gdsfmt_latest.tar.gz
wget --no-check-certificate https://github.com/zhengxwen/SeqArray/tarball/master -O SeqArray_latest.tar.gz
R CMD INSTALL gdsfmt_latest.tar.gz
R CMD INSTALL SeqArray_latest.tar.gz

## Or
curl -L https://github.com/zhengxwen/gdsfmt/tarball/master/ -o gdsfmt_latest.tar.gz
curl -L https://github.com/zhengxwen/SeqArray/tarball/master/ -o SeqArray_latest.tar.gz
R CMD INSTALL gdsfmt_latest.tar.gz
R CMD INSTALL SeqArray_latest.tar.gz
```

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

### Install Development Version from GitHub

Source: https://github.com/zhengxwen/seqarray/blob/master/README.md

Install the latest development versions of gdsfmt and SeqArray using devtools. Requires system compilers and make tools.

```R
library("devtools")
install_github("zhengxwen/gdsfmt")
install_github("zhengxwen/SeqArray")
```

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

### Install SeqArray via Bioconductor

Source: https://github.com/zhengxwen/seqarray/blob/master/README.md

Use BiocManager to install the package from the official Bioconductor repository.

```R
if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("SeqArray")
```

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

### Open and Inspect GDS File in R

Source: https://github.com/zhengxwen/seqarray/blob/master/README.md

Demonstrates how to load the SeqArray library, open a GDS file using a sample path, display its structure, and close the file connection.

```R
library(SeqArray)

gds.fn <- seqExampleFileName("gds")

# open a GDS file
f <- seqOpen(gds.fn)
# display the contents of the GDS file
f

# close the file
seqClose(f)
```

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

### GDS File Structure Output

Source: https://github.com/zhengxwen/seqarray/blob/master/README.md

The expected output format when displaying a SeqVarGDSClass object in the R console.

```R
## Object of class "SeqVarGDSClass"
## File: SeqArray/extdata/CEU_Exon.gds (298.6K)
## +    [  ] *
## |--+ description   [  ] *
## |--+ sample.id   { Str8 90 LZMA_ra(35.8%), 258B } *
## |--+ variant.id   { Int32 1348 LZMA_ra(16.8%), 906B } *
## |--+ position   { Int32 1348 LZMA_ra(64.6%), 3.4K } *
## |--+ chromosome   { Str8 1348 LZMA_ra(4.63%), 158B } *
## |--+ allele   { Str8 1348 LZMA_ra(16.7%), 902B } *
## |--+ genotype   [  ] *
## |  |--+ data   { Bit2 2x90x1348 LZMA_ra(26.3%), 15.6K } *
## |  |--+ ~data   { Bit2 2x1348x90 LZMA_ra(29.3%), 17.3K }
## |  |--+ extra.index   { Int32 3x0 LZMA_ra, 19B } *
## |  \--+ extra   { Int16 0 LZMA_ra, 19B }
## |--+ phase   [  ]
## |  |--+ data   { Bit1 90x1348 LZMA_ra(0.91%), 138B } *
## |  |--+ ~data   { Bit1 1348x90 LZMA_ra(0.91%), 138B }
## |  |--+ extra.index   { Int32 3x0 LZMA_ra, 19B } *
## |  \--+ extra   { Bit1 0 LZMA_ra, 19B }
## |--+ annotation   [  ]
## |  |--+ id   { Str8 1348 LZMA_ra(38.4%), 5.5K } *
## |  |--+ qual   { Float32 1348 LZMA_ra(2.26%), 122B } *
## |  |--+ filter   { Int32,factor 1348 LZMA_ra(2.26%), 122B } *
## |  |--+ info   [  ]
## |  |  |--+ AA   { Str8 1348 LZMA_ra(25.6%), 690B } *
## |  |  |--+ AC   { Int32 1348 LZMA_ra(24.2%), 1.3K } *
## |  |  |--+ AN   { Int32 1348 LZMA_ra(19.8%), 1.0K } *
## |  |  |--+ DP   { Int32 1348 LZMA_ra(47.9%), 2.5K } *
## |  |  |--+ HM2   { Bit1 1348 LZMA_ra(150.3%), 254B } *
## |  |  |--+ HM3   { Bit1 1348 LZMA_ra(150.3%), 254B } *
## |  |  |--+ OR   { Str8 1348 LZMA_ra(20.1%), 342B } *
## |  |  |--+ GP   { Str8 1348 LZMA_ra(24.4%), 3.8K } *
## |  |  \--+ BN   { Int32 1348 LZMA_ra(20.9%), 1.1K } *
## |  \--+ format   [  ]
## |     \--+ DP   [  ] *
## |        |--+ data   { Int32 90x1348 LZMA_ra(25.1%), 118.8K } *
## |        \--+ ~data   { Int32 1348x90 LZMA_ra(24.1%), 114.2K }
## \--+ sample.annotation   [  ]
##    \--+ family   { Str8 90 LZMA_ra(57.1%), 222B }
```
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