write.snps: Write genotype matrices to file, AlphaImpute style.
In stefanedwards/Siccuracy: Pipeline Package for AlphaImpute

Description Usage Arguments Details Value See Also

write.snps is short hand for write.table with some default options. For AlphaImpute format see Siccuracy.

Writes genotypes in VCF class objects to files in AlphaImpute-format.

write.snps(x, file, row.names = TRUE, na = "9", ...)

## S3 method for class 'matrix'
write.snps(x, file, row.names = TRUE, na = "9", ...)

## S3 method for class 'oxford'
write.snps(x, file, row.names = TRUE, na = "9", ...)

## S3 method for class 'haps'
write.snps(x, file, row.names = TRUE, na = "9", newID = 0,
  ...)

## S3 method for class 'vcfR'
write.snps(x, file, row.names = TRUE, na = "9", newID = 0,
  element = "GT", as.numeric = TRUE, convertNA = TRUE, ...)

`x`	The matrix to write.
`file`	Filename or connection to write to.
`row.names`	If genotype matrix is "raw" and has first column with animals IDs, set this to `FALSE`.
`na`	The string to use for `NA` in the data.
`...`	Passed on to write.table.
`newID`	... New ID, see `convert_plinkA`, but with some caveats here. I don't know.
`element`	element to extract from vcf genotype, see `extract.gt`.
`as.numeric`	logical, should the matrix be converted to numerics.
`convertNA`	logical indicating whether to convert "." to `NA` (see `na` for which value to use when writing to text file).

The new integer IDs can be supplied. If not, they will be made for you. newID may be an integer vector and will be used as is. If data.frame with columns sampID and newID, they will be reordered to match input file.

Returns data frame with ID mapping, truncated to those elements outputted.

write.table, connections.

write.snps

stefanedwards/Siccuracy documentation built on May 30, 2019, 10:44 a.m.