Write Sequoia Output to File

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 openxlsx).

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

if (FALSE) {
writeSeq(SeqList, OutFormat="xls", file="MyFile.xlsx")

# add additional sheet to the excel file:
library(openxlsx)
wb <- loadWorkbook("MyFile.xlsx")
addWorksheet(wb, sheetName = "ExtraData")
writeData(wb, sheet = "ExtraData", MyData, rowNames=FALSE)
saveWorkbook(wb, "MyFile.xlsx", overwrite=TRUE, returnValue=TRUE)

# or: (package requires java & is trickier to install)
xlsx::write.xlsx(MyData, file = "MyFile.xlsx", sheetName="ExtraData",
      col.names=TRUE, row.names=FALSE, append=TRUE, showNA=FALSE)
}