Checking and counting consecutive genes

Checking and counting consecutive genes

I want to check if there are gene clusters (consecutive genes with the same function) on each chromosome. So I have the gene genomic orders (coordinates), and function (pfam/gene family etc) for each gene.

R: use for loop to build a data frame

I wanted to test correlations between biological replicates of several samples in a ChIP-Seq experiment. Output better to be data frame with different features and samples.
GO enrichment in topGO using KS test

GO enrichment in topGO using KS test

The R package topGO can perform GO enrichment using Fisher's Exact test, which is based on gene counts, as well as Kolmogorov-Smirnov like test, which is based on gene scores.

ggplot in a loop

If you are using a for loop to output multiple plots, ggplot doesn't work.