uniqueFeatures: Table of features unique to a group

In HCBravoLab/metagenomeSeq: Statistical analysis for sparse high-throughput sequencing

Table of features unique to a group

Description

Creates a table of features, their index, number of positive samples in a group, and the number of reads in a group. Can threshold features by a minimum no. of reads or no. of samples.

Usage

uniqueFeatures(obj, cl, nsamples = 0, nreads = 0)

Arguments

obj	Either a MRexperiment object or matrix.
cl	A vector representing assigning samples to a group.
nsamples	The minimum number of positive samples.
nreads	The minimum number of raw reads.

Value

Table of features unique to a group

Examples

data(mouseData)
head(uniqueFeatures(mouseData[1:100,],cl=pData(mouseData)[,3]))

HCBravoLab/metagenomeSeq documentation built on March 17, 2024, 3:21 p.m.