cleanXM: Expression matrix cleaning tool

In genejockey33000/typGumbo: Scripts and Pipelines for RNAseq Analysis

Expression matrix cleaning tool

Description

This is a short pipeline that filters expression matrices based on k over A arguments, log2() transforms and quantile normalizes. Unnecessary for ratiometric data or previously processed data but useful for raw or TPM matrices. Function will remove all measurements with 0 values in all samples (zero variance). It will test matrix for asymmetric negative values (often resulting from regressing batch effects) and raise all values by abs(smallest negative value) to remove any negative expression measurement.

Usage

cleanXM(x, k = 0, A = 0)

Arguments

x	Input expression matrix, measurements in rows
k	Number of samples whose expression need to be higher than A
A	Expression (measurement) level to target

Value

cleaned expression matrix

genejockey33000/typGumbo documentation built on July 20, 2023, 11:45 p.m.