sequoia (version 2.3.5)

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.

See Also

writeColumns to write to a text file, using white space padding to keep columns aligned.

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)
# }
# NOT RUN {
# }