calcLogVal: Calculate log value of RNAseq columns

In rnaseqWrapper: Wrapper for several R packages and scripts to automate RNA-seq analysis

Description

Calculate the log value of a series of columns, allowing an offset to avoid returning "-Inf."

Usage

calcLogVal(data, colID = "FPKM", offset = 0.1,
           setBase = 2, matchEnd = TRUE)

Arguments

data	A matrix or data.frame containing gene (row) data for several individuals (columns).
colID	Either a numeric vector of columns to calculate the log of, or a character vector with patterns (e.g., FPKM) to match in the names of data. If a character vector, make sure the names are unique enough to match only what you want them to, as they will be called to grep.
offset	How much to add before taking log to avoid returning -Inf.
setBase	A positive number to pass to log to set the logarthimic base. Defaults to setBase = 2
matchEnd	Logical, should the colId pattern only match the end of the string.

Value

Returns a data.frame with the log value of the desired columns. Rows match the input data, so can be appended using cbind or merge.

Author(s)

Mark Peterson

Examples

## Only run if DESeq is available
if(require(DESeq)){

## Create sample data
## Could be reads or FPKM from your input
exampleCounts <- counts(makeExampleCountDataSet())

## Only calculate for the "2" columns
## This could be reads, if you have multiple column types
testLog <- calcLogVal(exampleCounts,
                      colID="2",
                      matchEnd=TRUE)
head(testLog)

## Calculate log of all columns
testLog2 <- calcLogVal(exampleCounts,
                       colID="*",
                       setBase=2)
head(testLog2)

}

rnaseqWrapper documentation built on May 2, 2019, 5:58 a.m.