fragment size distribution — fragSizeDist • ATACseqQC

estimate the fragment size of bams

fragSizeDist(
  bamFiles,
  bamFiles.labels,
  index = bamFiles,
  ylim = NULL,
  logYlim = NULL
)

Arguments

bamFiles	A vector of characters indicates the file names of bams.
bamFiles.labels	labels of the bam files, used for pdf file naming.
index	The names of the index file of the 'BAM' file being processed; This is given without the '.bai' extension.
ylim	numeric(2). ylim of the histogram.
logYlim	numeric(2). ylim of log-transformed histogram for the insert.

Value

Invisible fragment length distribution list.

Author

Jianhong Ou

Examples

bamFiles <- dir(system.file("extdata", package="ATACseqQC"), "GL.*.bam$", full.names=TRUE)
bamFiles.labels <- sub(".bam", "", basename(bamFiles))
fragSizeDist(bamFiles, bamFiles.labels)