rnaseqWrapper (version 1.0-1)

calculateThirdPosBias: Calculate the third position bias of polymorphisms

Description

Determines which variant positions are in the third codon position, or estimates that based on frequency, and reports the proportion of variants in each gene that are in the third position.

These are presumed to be synonomous more often, but if codon information is known, users should run determineSynonymous instead.

Usage

calculateThirdPosBias(varTable, seqIDcol = 1, refPosCol = "Reference.Position", readCutoffs = 0, colprepend = "nVar_", codonStartPos = NULL)

Arguments

varTable

A data.frame with rows for each position in each gene with a variant present. Columns give various information for each included individual. This is expecting the format from readVariantFiles, which should be easy to emulate

seqIDcol

Which column is the sequence ID in? Can be numeric or character.

refPosCol

Which column is the referencece position in? Can be numeric or character.

readCutoffs

How many variable positions need to be present to calculate bias. Set to 1 (or 0 or NULL) to include all. Without a reference, small numbers will be almost meaningless.

colprepend

What name should the output columns be prepended with

codonStartPos

If "cds" assumes all start at position 1 (default). If NULL, will treat the frame as unknown and assign the most frequent position as the putative third position. In the future, can be a vector giving which position each gene starts at; currently not handled.

Value

Returns a matrix with genes as rows and with the number of variants in each position and proportion of variants in the third position as columns.

See Also

readVariantFiles, determineSynonymous

Examples

## Load example data
data(varScanExample)

calculateThirdPosBias(varScanExample,
                      refPosCol="Position",
                      codonStartPos="cds")