humarray (version 1.2)

compact.gene.list: Make a compact version of gene annotation

Description

When adding gene annotation to genomic ranges, sometimes there are many genes associated with a single feature, so that compiling a table becomes awkward, if some rows contain hundreds of genes. This function takes a character vector of gene lists delimited by some separator and provides a compact representation of the gene labels

Usage

compact.gene.list(x, n = 3, sep = ";", others = FALSE)

Arguments

x

is a character vector of gene label listings, where multiple hits are delimited by 'sep'

n

number of genes to list before abbreviating

sep

character, separator used to delimit genes in elements of x

others

logical, TRUE to abbreviate with '+ # others' or FALSE to append just the number of genes not listed.

Value

a character vector with the form: gene-1, gene-2, ..., gene-n, + length(gene-n) - n [others]

Examples

# NOT RUN {
my.genes <- c("ERAP1","HLA-C;CTLA4;IFIH","INS;MYC","AGAP1;APOE;DRDB1;FUT2;HCP5;BDNF;COMT")
compact.gene.list(my.genes)
compact.gene.list(my.genes,n=2,others=TRUE)
# }