dumpBaseline: Export GSI baseline file

Description Usage Arguments Author(s)

View source: R/dumpBaseline.r

Description

dumpBaseline() exports a gsi baseline file in BAYES, SPAM, or gsi_sim format

Usage

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dumpBaseline(x, markers, fileType, filename, findMarkers = NULL,
  replaceWith = NULL, removePrefix = NULL, replaceBP = TRUE,
  basePairs = c("A", "C", "G", "T", "-"), replacements = c("1", "2", "3",
  "4", "5"))

Arguments

x

the list of populations to be included in gsi baseline file

markers

the markers to be included in gsi baseline file

fileType

the format of the exported gsi baseline file. Can be set to "SPAM", "BAYES", or "gsi_sim"

filename

what would you like to name the exported gsi baseline file

findMarkers

i don't remember what this does, just leave as the default NULL

replaceWith

something related to findMarkers. Also leave as the default NULL

removePrefix

this can be used to trim the marker names for "SPAM"

replaceBP

would you like to replace the allele names with something else. By default, dumpBaseline() replaces c("A","C","G","T","-") with c("1","2","3","4","5"). This can be set to "FALSE" to keep data in the original imported format. Alternatively, the basePairs and replacements arguments can be modified to accommodate any desired import or export format.

basePairs

If replaceBP = TRUE, the nomenclature used for the imported genotype data

replacements

If replaceBP = TRUE, what would you like to replace the alleles with?

Author(s)

Eric Grau and Mike Ackerman


mackerman44/idfgen documentation built on May 21, 2017, 4:46 p.m.