readLengthTable {ORFik} | R Documentation

## Make table of readlengths

### 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`. You can also add a time remaining bar, for a more detailed pipeline.

### 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")`

[Package ORFik version 1.12.13 Index]