zTransformDirectory: Z-score transformation of DAVID functional annotation charts...

In awaardenberg/CompGO: An R pipeline for .bed file annotation, comparing GO term enrichment between gene sets and data visualisation

Description

Given a directory of functional annotation charts, this function iterates over them and generates Odds Ratio, St. Error and Z scores. This is useful for batch processing, as all the charts can be written to disk somewhere then iterated over by this function automatically. Two options are provided for dealing with absent terms: either the NAs are set as 0 (a pseudo-representation of a Z-score with no enrichment), or incomplete rows are removed. The final table can be used for clustering analyses.

Usage

zTransformDirectory(inputDir, cutoff = NULL, pattern = NULL,
  removeNA = FALSE)

Arguments

inputDir	The directory to search for functional annotation charts
pattern	The regex pattern to match files in inputDir
cutoff	Reduce the computation to the top n GO terms ranked by variance
removeNA	True to only generate the Z-transform table based on GO terms common to all input enrichment analyses, False to set all NAs as 0

Value

Returns a data.frame of z scores, ORs and SEs

Examples

## Not run: 
#not run as dir required
z.merge = zTransformDirectory("./fnAnot_charts", pattern = "-fnAnot.txt")
# To plot a dendrogram based on Z-scores:
d <- cor(abs(z.merge[2:(ncol(z.merge)-1)]))
dist.cor <- hclust(dist(1-d), method="complete")
plot(dist.cor, xlab="Complete linkage", sub = NA)

## End(Not run)

awaardenberg/CompGO documentation built on May 11, 2019, 4:08 p.m.