countSymbols: countSymbols

Description Usage Arguments Details See Also Examples

Description

Counts unique symbols from an expression table.

Usage

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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

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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.