-First of all my map file is not sorted on chromosome, I understand that this is not an issue as long as the map file align with the order of the ped file?
Here is how the first lines look:
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25 BICF2G630100019 0 31558578
25 BICF2G630100032 0 31570089
25 BICF2G630100034 0 31571436
25 BICF2G630100043 0 31596554
25 BICF2G630100054 0 31614639
25 BICF2G630100063 0 31625208
25 BICF2G630100075 0 31648688
39 BICF2G63010009 94.52299 92315155
25 BICF2G630100090 0 31698243
25 BICF2G630100094 0 31699552
There is no problem loading the map- and ped file with convert.snp.ped with these 4 columns and no header, however R quits without giving me an error code if I try to use the same map file with 3 columns and header like this (I have changed the mapHasHeaderLine accordingly):
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chrom name position
25 BICF2G630100019 31558578
25 BICF2G630100032 31570089
25 BICF2G630100034 31571436
25 BICF2G630100043 31596554
25 BICF2G630100054 31614639
25 BICF2G630100063 31625208
25 BICF2G630100075 31648688
39 BICF2G63010009 92315155
25 BICF2G630100090 31698243
25 BICF2G630100094 31699552
And here is a part of the ped file:
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54 SAR02 0 0 0 0 C C T C A G A A T T T T T T A G C C T T T T C C T T 0 0 C C A A A C C C T T T C C C A A C C G G C C A A G G T T C C T T A
Any ideas?