degFilter: Filter genes by group

In lpantano/DEGreport: Report of DEG analysis

Filter genes by group

Description

This function will keep only rows that have a minimum counts of 1 at least in a min number of samples (default 80%).

Usage

degFilter(counts, metadata, group, min = 0.8, minreads = 0)

Arguments

counts	Matrix with expression data, columns are samples and rows are genes or other feature.
metadata	Data.frame with information about each column in counts matrix. Rownames should match colnames(counts).
group	Character column in metadata used to group samples and applied the cutoff.
min	Percentage value indicating the minimum number of samples in each group that should have more than 0 in count matrix.
minreads	Integer minimum number of reads to consider a feature expressed.

Value

count matrix after filtering genes (features) with not enough expression in any group.

Examples

data(humanGender)
library(SummarizedExperiment)
idx <- c(1:10, 75:85)
c <- degFilter(assays(humanGender)[[1]][1:1000, idx],
  colData(humanGender)[idx,], "group", min=1)

lpantano/DEGreport documentation built on Feb. 28, 2024, 12:01 a.m.