pairs2pi0s: pairs2pi0s

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

pairs2pi0s

Description

Function to estimate and plot the proportion of null features from pairwise TER tests.

Function to estimate and plot the proportion of null features from pairwise TER tests.

Usage

pairs2pi0s(x, outfile = NULL)

pairs2pi0s(x, outfile = NULL)

Arguments

x	A list of the results of TER tests between all pairs of samples in a data set produced by TER_all_pairs.
outfile	The path and name of the output pdf file. Default: NULL.
x	A list of the results of TER tests between all pairs of samples in a data set produced by TER_all_pairs.
outfile	The path and name of the output pdf file. Default: NULL.

Details

A histogram of pi0s is created colored by pair type. If outfile is given, the histogram will be saved to the pdf file, too. "Homo" pairs are expected to have a higher proportion of null features than "Hetero" pairs.

A histogram of pi0s is created colored by pair type. If outfile is given, the histogram will be saved to the pdf file, too. "Homo" pairs are expected to have a higher proportion of null features than "Hetero" pairs.

Value

A data frame describing uniqueIDs and groupIDs of pairs of compared samples, the pair_type ("Homo" or "Hetero") and the estimated pi0 (proportion of null features aka not differentially translated transcripts).

A data frame describing uniqueIDs and groupIDs of pairs of compared samples, the pair_type ("Homo" or "Hetero") and the estimated pi0 (proportion of null features aka not differentially translated transcripts).

Examples

pi0df_LMCN <- pairs2pi0s(rr_LMCN.v2.pairwise)
pi0df_LMCN <- pairs2pi0s(rr_LMCN.v2.pairwise)

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