log2Tran: Log Transforms a data frame

In roonysgalbi/tispec: Calculates tissue specificity from RNA-seq data

Description

Adds a pseudocount (1e-10) to remove zeros, then log2 transforms each column independently. This normalises the data frame within each column only (not across columns - see tispec::QuantNorm). After log2 transformation, it resets all negative values to zero, thus setting a noise threshold of log2(1). Finally it removes all rows where every column is 0 (i.e. below threshold, removing genes not expressed in any tissue)

Usage

log2Tran(x)

Arguments

x	data frame of mean expression (cells) of genes (rows) in tissues (columns)

Value

Returns a data frame of log2 normalised counts, with non-expressed genes (rows) removed

Examples

head(meanExp)
log2Exp <- log2Tran(meanExp)
head(log2Exp)

roonysgalbi/tispec documentation built on May 26, 2019, 1:33 a.m.