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Bugfix: manhattan.R now indexes with BP, not SNP which should be an optional column #72

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Bugfix: manhattan.R now indexes with BP, not SNP which should be an optional column #72

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2 changes: 1 addition & 1 deletion R/manhattan.R
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Original file line number Diff line number Diff line change
Expand Up @@ -95,7 +95,7 @@ manhattan <- function(x, chr="CHR", bp="BP", p="P", snp="SNP",
# ind = ind + 1
# d[d$CHR==i,]$index = ind
# }
d$index = rep.int(seq_along(unique(d$CHR)), times = tapply(d$SNP,d$CHR,length)) # replcace the for loop of line 92-96 to improve efficiency
d$index = rep.int(seq_along(unique(d$CHR)), times = tapply(d$BP,d$CHR,length)) # replcace the for loop of line 92-96 to improve efficiency

# This section sets up positions and ticks. Ticks should be placed in the
# middle of a chromosome. The a new pos column is added that keeps a running
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