psite_rW: psite_rW

In goodarzilab/Ribolog: Logistic-regression-based analysis of ribosome profiling data

psite_rW

Description

Function to calculate the most likely position of p-site for each read length group.

Usage

psite_rW(reads_list, flanking = 6, start = TRUE, extremity = "auto",
  plot = FALSE, plot_dir = NULL, plot_format = "png", cl = 99)

Arguments

reads_list	A reads_list object produced by bamtolist_rW
flanking	Minimum number of nucleotides that have to flank the target codon in both directions. Default: 6.
start	Logical argument indicating whether to use the start codon as reference. Default: TRUE. If set to FALSE, the second to last codon is used.
extremity	"5end", "3end" or "auto": the read end on which the correction step should be based. Default: "auto".
plot	Whether read-length-specific ribosome occupancy plots are produced. Default: FALSE.
plot_dir	The directory where the read-length-specific ribosome occupancy plots are saved. This argument is only considered if plot = TRUE.
plot_format	"png" or "pdf". It is only considered if plot = TRUE.

Value

The output is a data table, containing for all samples and read lengths the percentage of reads in the dataset, the percentage of reads aligning to the start codon, and the distance of p-site from the two read extremities.

Examples

psite_offset_LMCN <- psite_rW(reads_list_LMCN)

goodarzilab/Ribolog documentation built on Oct. 7, 2022, 10:14 p.m.