sequoia: writeSeq – R documentation

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writeSeq

Write Sequoia Output to File

Description

The various list elements returned by sequoia are each written to text files in the specified folder, or to separate sheets in a single excel file (requires library xlsx).

Usage

writeSeq(
  SeqList,
  GenoM = NULL,
  MaybeRel = NULL,
  PedComp = NULL,
  OutFormat = "txt",
  folder = "Sequoia-OUT",
  file = "Sequoia-OUT.xlsx",
  ForVersion = 2,
  quiet = FALSE
)

Arguments

`SeqList`	list returned by `sequoia`, to be written out.
`GenoM`	matrix with genetic data (optional). Ignored if OutFormat='xls', as the resulting file could become too large for excel.
`MaybeRel`	list with results from `GetMaybeRel` (optional).
`PedComp`	list with results from `PedCompare` (optional). `SeqList$DummyIDs` is combined with `PedComp$DummyMatch` if both are provided.
`OutFormat`	'xls' or 'txt'.
`folder`	the directory where the text files will be written; will be created if it does not already exists. Relative to the current working directory, or NULL for current working directory. Ignored if `OutFormat='xls'`.
`file`	the name of the excel file to write to, ignored if `OutFormat='txt'`.
`ForVersion`	choose '1' for back-compatibility with stand-alone sequoia versions 1.x
`quiet`	suppress messages.

Details

The text files can be used as input for the stand-alone Fortran version of sequoia, e.g. when the genotype data is too large for R. See vignette('sequoia') for further details.

Examples

## Not run: 
writeSeq(SeqList, OutFormat="xls", file="MyFile.xlsx")

# add additional sheets to the excel file:
library(xlsx)
write.xlsx(MyData, file = "MyFile.xlsx", sheetName="ExtraData",
      col.names=TRUE, row.names=FALSE, append=TRUE, showNA=FALSE)

## End(Not run)

sequoia

Pedigree Inference from SNPs

v2.3.3

GPL-2

Authors

Jisca Huisman [aut, cre]

Initial release

2021-04-30