Question: Rehh package input files
gravatar for kas
14 months ago by
kas0 wrote:

Dear respected members, How to make "map.inp" files for running rehh? I have .ped and .map files from plink. I have got the haplotype information from fastPHASE (hapguess_switch.out).

Thank you in advance.

map.inp rehh R • 351 views
ADD COMMENTlink written 14 months ago by kas0

Did you read the manual?

It is a simple text file, example from the manual:

# show first 6 lines of file
cat(readLines("map.inp", n = 6), sep = "\n")
> F0100190 1 113642 T A
> F0100220 1 244699 C G
> F0100250 1 369419 G C
> F0100270 1 447278 A T
> F0100280 1 487654 T A
> F0100290 1 524507 C G
ADD REPLYlink modified 14 months ago • written 14 months ago by zx87549.7k

Thank you for your response. I've read the manual. Here totally 5 columns are there. Last 2 for ancestral and derived alleles. But I don't have that information. How to get those ancestral and derived alleles?

If I load my map file in R, It's showing like this

Error in read.table(map_file, row.names = 1, colClasses = "character") :
  duplicate 'row.names' are not allowed.

This is my map file format.

rs41609588  chr1    135098
rs108982244 chr1    267940
rs43703977  chr1    393248
rs110887329 chr1    471078
rs29015852  chr1    516404
rs110936909 chr1    571340
rs108981857 chr1    845494
ADD REPLYlink modified 14 months ago by zx87549.7k • written 14 months ago by kas0
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