gbsrGDS2CSV | R Documentation |
Write out a CSV file with raw, filtered, corrected genotype data or estimated haplotype data stored in a GDS file.
gbsrGDS2CSV(
object,
out_fn,
node = "raw",
incl_parents = TRUE,
bp2cm = NULL,
format = "",
read = FALSE,
...
)
## S4 method for signature 'GbsrGenotypeData'
gbsrGDS2CSV(object, out_fn, node, incl_parents, bp2cm, format, read)
object |
A GbsrGenotypeData object. |
out_fn |
A string to specify the path to an output VCF file. |
node |
Either one of "raw", "filt", "cor", and "hap" to output raw genotype data, filtered genotype data, corrected genotype data, estimated haplotype data, respectively. |
incl_parents |
A logical value to specify whether parental samples should be included in an output VCF file or not. |
bp2cm |
A numeric value to convert positions in basepairs (bp) to
centiMorgan (cm). The specified here is used to multiply position values. The
default is NULL and then internally sets |
format |
A string to indicate the output format. See details. |
read |
A logical value to indicate whether read counts should be output with genotype data or not. See details. |
... |
Unused. |
Create a CSV file at location specified by out_fn. The current
implementation only changes the behavior when format = "qtl"
to export
the data in the r/qtl format that can be loaded using read.cross as
format = "csvs
with a phenotype data. Any other values are ignored and
output a CSV file with the rows indicating chromosome ID and positions of
markers followed by the rows indicating genotype or haplotype data of
samples. If read = TRUE
, the output of each genotype call would be in
the form of GT:ADR,ADA
where GT, ADR, and ADA represent genotype,
referenece read count, and alternative read count, respectively.
If format = "qtl"
, read = TRUE
will be ignored.
The path to the CSV file.
# Load data in the GDS file and instantiate a [GbsrGenotypeData] object.
gds_fn <- system.file("extdata", "sample.gds", package = "GBScleanR")
gds <- loadGDS(gds_fn)
# Create a CSV file with data from the GDS file
# connected to the [GbsrGenotypeData] oobject.
out_fn <- tempfile("sample_out", fileext = ".csv")
gbsrGDS2CSV(gds, out_fn)
# Close the connection to the GDS file.
closeGDS(gds)
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