readTagDigger: Import Read Counts from TagDigger

In lvclark/polyRAD: Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids

Import Read Counts from TagDigger

Description

readTagDigger reads the CSV output containing read counts from TagDigger and generates a "RADdata" object. Optionally, it can also import a tag database generated by the Tag Manager program within TagDigger, containing information such as alignment position, to be stored in the $locTable slot of the "RADdata" object.

Usage

readTagDigger(countfile, includeLoci = NULL, 
              possiblePloidies = list(2), taxaPloidy = 2L,
              contamRate = 0.001,
              dbfile = NULL, dbColumnsToKeep = NULL, 
              dbChrCol = "Chr", dbPosCol = "Pos", 
              dbNameCol = "Marker name")

Arguments

countfile	Name of the file containing read counts.
includeLoci	An optional character vector containing names of loci to retain in the output.
possiblePloidies	A list of numeric vectors indicating potential inheritance modes of SNPs in the dataset. See RADdata.
taxaPloidy	A single integer, or an integer vector with one value per taxon, indicating ploidy. See RADdata.
contamRate	A number ranging from zero to one (typically small) indicating the expected rate of sample cross-contamination.
dbfile	Optionally, name of the Tag Manager database file.
dbColumnsToKeep	Optionally, a character vector indicating the names of columns to keep from the database file.
dbChrCol	The name of the column containing the chromosome number in the database file.
dbPosCol	The name of the column indicating alignment position in the database file.
dbNameCol	The name of the column containing marker names in the database file.

Details

Nucleotides associated with the alleles, to be stored in the $alleleNucleotides slot, are extracted from the allele names in the read counts file. It is assumed that the allele names first contain the marker name, followed by an underscore, followed by the nucleotide(s) at any variable positions.

Value

A "RADdata" object.

Author(s)

Lindsay V. Clark

References

https://github.com/lvclark/tagdigger

Clark, L. V. and Sacks, E. J. (2016) TagDigger: User-friendly extraction of read counts from GBS and RAD-seq data. Source Code for Biology and Medicine 11, 11.

See Also

readHMC, readStacks, VCF2RADdata, readTASSELGBSv2, readDArTag

Examples

# for this example we'll create dummy files
countfile <- tempfile()
write.csv(data.frame(row.names = c("Sample1", "Sample2", "Sample3"),
                     Mrkr1_A_0 = c(0, 20, 4),
                     Mrkr1_G_1 = c(7, 0, 12)),
          file = countfile, quote = FALSE)
dbfile <- tempfile()
write.csv(data.frame(Marker.name = "Mrkr1", Chr = 5, Pos = 66739827),
          file = dbfile, row.names = FALSE, quote = FALSE)

# read the data
myrad <- readTagDigger(countfile, dbfile = dbfile)

lvclark/polyRAD documentation built on Jan. 15, 2024, 4:19 a.m.