readLengthTable: Make table of readlengths

In ORFik: Open Reading Frames in Genomics

Description

Summarizing all libraries in experiment, make a table of proportion of read lengths.

Usage

readLengthTable(df, output.dir = NULL, type = "ofst", BPPARAM = bpparam())

Arguments

df	an ORFik experiment
output.dir	NULL or character path, default: NULL, plot not saved to disc. If defined saves plot to that directory with the name "./readLengths.csv".
type	character, default: "ofst". Type of library: either "default", usually bam format (the one you gave to experiment), "pshifted" pshifted reads, "ofst", "bed", "bedo" optimized bed, or "wig"
BPPARAM	how many cores/threads to use? default: bpparam(). To see number of threads used, do bpparam()$workers

Value

a data.table object of the the read length data with columns: c("sample", "sample_id", "read length", "counts", "counts_per_sample", "perc_of_counts_per_sample")

ORFik documentation built on March 27, 2021, 6 p.m.