convertToAllelicFractions: Convert read counts across read groups to relative fractions...

In SNPhood: SNPhood: Investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data

Description

convertToAllelicFractions convert read counts across read groups to their relative fractions among all read groups (all read counts will be between 0 and 1, with 1 for a particular read group depicting that all reads from this particular position originate from the one read group) Affected slots are readCountsUnbinned and readCountsBinned. It is recommended to save the resulting SNPhood object with a new name because it is not possible to go back from fractions to read counts at a later point.

Usage

convertToAllelicFractions(SNPhood.o, roundDigits = 2, setNaNToZero = FALSE,
  verbose = TRUE)

Arguments

SNPhood.o	Object of class SNPhood
roundDigits	Numeric(1). Default 2. Number of digits after the decimal place when converting read counts to fractions
setNaNToZero	Logical(1). Default FALSE. Should NaN (not a number) be converted to 0? NaN may result from individual regions or bins with no reads across all read groups due to a division by zero.
verbose	Logical(1). Default TRUE. Should the verbose mode (i.e., diagnostic messages during execution of the script) be enabled?

Value

an object of class SNPhood with read counts across read groups (both for the slots readCountsUnbinned and readCountsBinned) replaced by their respective relative fractions. Otherwise identical to the input SNPhood object.

See Also

deleteReadGroups

Examples

data(SNPhood.o, package="SNPhood")
SNPhood_allelicFractions.o = convertToAllelicFractions(SNPhood.o)

# Convert all NaN to 0 for subsequent analyses
SNPhood_allelicFractions.o = convertToAllelicFractions(SNPhood.o, setNaNToZero = TRUE)

SNPhood documentation built on Nov. 8, 2020, 6:22 p.m.