export.merlin {GenABEL} | R Documentation |
Exports GenABEL data to Merlin and other pedigree formats
export.merlin(data, pedfile = "merlin.ped", datafile = "merlin.dat", mapfile = "merlin.map", format = "merlin", fixstrand = "no", extendedmap = TRUE, traits = 1)
data |
gwaa.data object |
pedfile |
Output pedigree data file name |
datafile |
Output data (information) file name |
mapfile |
Output map file name |
format |
Output format: reserved for future use, currently only "merlin" |
fixstrand |
"no" – the strand information and coding comes from the data; "+" – change all coding to "+" strand, "-" – change all coding to "-" strand |
extendedmap |
if TRUE extended map (+ strand, + coding) is saved with the name "mapfile.ext", where "mapfile" is the parameter supplied by user |
traits |
How many fake traits to insert before first column of marker data |
The use is straightforward, with only the "fixstrand" option requiring some explanation. Consider a SNP on "-" strand with alleles G and A. If this SNP is accessed on "+" strand, the corresponding alleles would be C and T. While for example Affymetrix reports SNPs on bot "+" and "-" strands, HapMap reports coding on "+" strand only. To make data compatible, and/or to run imputations, one will need to convert all SNP codes to "+" strand. This can be achieved by running export.merlin() with fixstrand="+" parameter.
No value returned
Yurii Aulchenko
To load the data to GenABEL again, use convert.snp.ped
,
load.gwaa.data
.
# # load(srdta) # export.merlin(srdta[1:50,1:3]) #