readDat and readAfreq read data and population allele
frequencies from csv files and reformat them for further processing.
formatDat and formatAfreq reformat corresponding data frames.
Original data are assumed to be in a long format, with one row per allele.
Usage
readDat(sfile, svar, lvar, avar, ...)
formatDat(dlong, svar, lvar, avar)
readAfreq(afile, lvar, avar, fvar, ...)
formatAfreq(aflong, lvar, avar, fvar)Arguments
- sfile
the name of the file containing sample data.
- svar
the name of the variable for sample ID.
- lvar
the name of the variable for locus/marker.
- avar
the name of the variable for allele/haplotype.
- ...
additional arguments for
read.csv().- dlong
a data frame containing sample data.
- afile
the name of the file containing population allele frequencies.
- fvar
the name of the variable for population allele frequiency.
- aflong
a data frame containing population allele frequencies.
Value
For readDat and formatDat, a list with elements
corresponding to samples. Each element of the list is itself a list of
binary vectors, one vector for each locus. For readAfreq and
formatAfreq, a list with elements corresponding to loci. The
frequencies at each locus are normalized and sum to 1. Samples, loci, and
alleles are ordered by their IDs/names.
See also
matchAfreq for making sure that the list containing
sample data is conformable to provided population allele frequencies.
Examples
sfile <- system.file("extdata", "MozParagon.csv", package = "dcifer")
dsmp <- readDat(sfile, svar = "sampleID", lvar = "locus", avar = "allele")
# OR, if the dataset is provided as an R data frame, e.g.
dlong <- read.csv(sfile)
# reformat only:
dsmp <- formatDat(dlong, svar = "sampleID", lvar = "locus", avar = "allele")
afile <- system.file("extdata", "MozAfreq.csv", package = "dcifer")
afreq2 <- readAfreq(afile, lvar = "locus", avar = "allele", fvar = "freq")
# OR, if allele frequencies are provided as an R data frame, e.g.
aflong <- read.csv(afile)
# reformat only:
afreq2 <- formatAfreq(aflong, lvar = "locus", avar = "allele", fvar = "freq")
dsmp2 <- matchAfreq(dsmp, afreq2)