listSymbols: listSymbols

In charles-plessy/smallCAGEqc: ad-hoc QC functions for shallow-sequenced test CAGE libraries

Description

List unique gene symbols, which some can be comma-separated.

Usage

listSymbols(...)

Arguments

...

Vector(s) or list(s) of character strings. Multiple genes can overlap at a given position on the genome. Therefore, it is hard to associate directly a single-base TSS to a single gene symbol. In our workflows we prepare gene expression tables where TSS counts are pooled per gene symbol. If a position belongs to more than one gene, an artificial ad-hoc symbol is created by concatenating the symbols with commas. For instance, ‘7SK,ACTR5’. As a result, one can not infer the number of detected genes by simply counting the number of rows where expression is igher that zero. listSymbols is the solution to that problem. It will concatenate with commas a list of row names from such gene expression tables, and then expand it again and remove duplicates. That is, ‘"7SK,ACTR5", "7SK,ADAM10"’ becomes ‘"7SK,ACTR5,7SK,ADAM10"’ and then ‘"7SK" ,ACTR5", "ADAM10"’. listSymbols will also search and remove the “.” gene symbol, which is a special artefact of our workflows.

Details

Takes a serie of strings containing either one gene symbol or comma-separated gene symbols, character vector of unique gene symbols.

Value

Returns a vector of unique character strings, or NULL if the input contained no strong, the empty string alone, or the special symbol “.”.

Examples

listSymbols("7SK,ACTR5", "7SK,ADAM10")
length(listSymbols("7SK,ACTR5", "7SK,ADAM10"))
listSymbols("")
length(listSymbols(""))

charles-plessy/smallCAGEqc documentation built on May 13, 2019, 3:31 p.m.