sequoia (version 1.3.1)

writeSeq: write sequoia output to excel or text files

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, PedComp = NULL, OutFormat = "txt",
  folder = "Sequoia-OUT", file = "Sequoia-OUT.xlsx", quiet = FALSE)

Arguments

SeqList

the list returned by sequoia, to be written out.

GenoM

the matrix with genetic data (optional). Ignored if OutFormat='xls', as the resulting file could become too large for excel.

PedComp

a 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'.

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)
# }
# NOT RUN {
# }