getBamInfo: Obtain library information from BAM files
In ldg21/SGSeq: Splice event prediction and quantification from RNA-seq data

Description Usage Arguments Details Value Author(s) Examples

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

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

`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

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.

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

Leonard Goldstein

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)