getBamInfo {SGSeq} | R Documentation

## Obtain library information from BAM files

### Description

Obtain paired-end status, median aligned read length, median aligned insert size and library size from BAM files.

### Usage

    getBamInfo(sample_info, yieldSize = NULL, cores = 1)

### Arguments

`sample_info` | Data frame with sample information including mandatory columns “sample_name” and “file_bam”. Column “sample_name” must be a character vector. Column “file_bam” can be a character vector or `BamFileList`.
`yieldSize` | Number of records used for obtaining library information, or `NULL` for all records
`cores` | Number of cores available for parallel processing

### Details

BAM files must have been generated with a splice-aware alignment program that outputs the custom tag ‘XS’ for spliced reads, indicating the direction of transcription. BAM files must be indexed.

Library information can be inferred from a subset of BAM records by setting the number of records via argument `yieldSize`. Note that library size is only obtained if `yieldSize` is NULL.

### Value

`sample_info` with additional columns “paired_end”, “read_length”, “frag_length”, and “lib_size” if `yieldSize` is `NULL`

### Author(s)

Leonard Goldstein

### Examples

    path <- system.file("extdata", package = "SGSeq")
    si$file_bam <- file.path(path, "bams", si$file_bam)

    ## data.frame as sample_info and character vector as file_bam
    si <- si[, c("sample_name", "file_bam")]
    si_complete <- getBamInfo(si)

    ## DataFrame as sample_info and BamFileList as file_bam
    DF <- DataFrame(si)
    DF$file_bam <- BamFileList(DF$file_bam)
    DF_complete <- getBamInfo(DF)

[Package SGSeq version 1.18.0 Index]