After process_isoloci.py is used to assign RAD tags to alignment locations
within a highly duplicated genome, readProcessIsoloci
imports the
resulting CSV to a "RADdata"
object.
readProcessIsoloci(sortedfile, min.ind.with.reads = 200,
min.ind.with.minor.allele = 10,
min.median.read.depth = 10,
possiblePloidies = list(2),
contamRate = 0.001,
nameFromTagStart = TRUE, mergeRareHap = TRUE)
File path to a CSV output by process_isoloci.py.
Minimum number of individuals with reads needed to retain a locus.
Minimum number of individuals with reads in a minor allele needed to retain a locus.
Minimum median read depth across individuals (including individuals with depth 0) needed to retain a locus.
A list indicating possible inheritance modes of loci. See RADdata
.
Approximate rate of cross-contamination among samples.
If TRUE
loci will be named based on the alignment position and strand
of the RAD tag itself. If FALSE
, loci will be named based on the leftmost
position of the variable region of the RAD tag. In either case,
locTable$Pos
within the output will indicate the position of the variable
region of the tag.
Boolean indicating whether to run MergeRareHaplotypes
after
building the "RADdata"
object.
A "RADdata"
object containing read depth and alignment positions
from sortedfile
.
MergeIdenticalHaplotypes
is used internally by this function to
merge alleles with identical sequence for the region shared by all tags, in
cases where tags vary in length within a locus.