convertToAllelicFractions {SNPhood} | R Documentation |
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.
convertToAllelicFractions(SNPhood.o, roundDigits = 2, setNaNToZero = FALSE, verbose = TRUE)
SNPhood.o |
Object of class |
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? |
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.
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)