r - Replace different values in one column, according to the row information in another column -


i working genomic data, , have 1 data frame, going show first 3 rows (see table below):

chrom |   pos    |     id      | ref | alt | hapa | hapb | ----------------------------------------------------------  22   | 16495833 | rs116911124 |   |  c  |   1  |  0   |  22   | 19873357 | rs116378360 |  t  |   |   0  |  1   |  22   | 21416404 | rs117982183 |  t  |  t  |   0  |  .   |

so, replace values of "0", "1" , "." "hapa" , "hapb" columns according ref , alt columns every row in data frame. example:

a) first row want change "1" in hapa column "c" in alt column, , "0" in hapb column "a" value in ref column

b) second row change "0" "t" in "ref" column , "1" "a" in "alt" column.

c) , finally, "." change "na"

i think achieved using "if else" or data.table.

thank much.

it's bit unclear want exactly, since don't specify should happen 0 in third row of hapa column, given said, dplyr solution:

library(dplyr)  df <- read.table(text = " 'chrom'     'pos'      'id'       'ref'  'alt' 'hapa' 'hapb' 22     16495833   'rs116911124'    'a'     'c'      1     0   22     19873357   'rs116378360'    't'     'a'      0     1   22     21416404   'rs117982183'    't'     't'      0     .", header = t, stringsasfactors = f)  df %>%   mutate(hapa = ifelse(hapa == 1, alt, ifelse(hapa == 0, ref, na)),          hapb = ifelse(hapb == 1, alt, ifelse(hapb == 0, ref, na)))  ##   chrom      pos          id ref alt hapa hapb ## 1    22 16495833 rs116911124     c    c    ## 2    22 19873357 rs116378360   t      t    ## 3    22 21416404 rs117982183   t   t    t <na>

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