countSymbols: countSymbols

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

Description

Counts unique symbols from an expression table.

Usage

countSymbols(TABLE)

Arguments

TABLE

An expression table

Details

Takes an expression table and returns the number of detected genes for each library.

Returns a named numeric vector where each element is the number of different symbols found to be expressed in a given sample. In the expression table, columns represent samples and rows represent symbols. Some rows can represent multiple samples, typically when a CAGE tag overlaps with more than one reference transcript for different genes. In that case, the row names are made of a comma-separated list of symbols. Thus, a symbol can be found on multiple rows. This is why this function is needed.

See Also

codelistSymbols

Examples

exp.tbl <- data.frame( sample1=c(1,2), sample2=c(1,0), sample3=c(0,0)
                     , row.names=c("A", "A,B"))
countSymbols(exp.tbl)

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