if else statement adjustemtn

b[is.na(b$FLASER) | is.na(b$PLASER),]

Since you have only a few troublesome NA values, if you look at them,
or even better, post them:

b[is.na(b$FLASER) | is.na(b$PLASER),]

perhaps we can work out the appropriate logic to get rid of only the
ones you don't want.

Jim

On Sat, Jun 13, 2020 at 12:50 PM Ana Marija <sokovic.anamarija at gmail.com> wrote:

Hi Rasmus,

thank you for getting back to be, the command your provided seems to
add all 11 NAs to 2s

b$pheno <-

+           ifelse(b$PLASER==2 |
+                  b$FLASER==2 |
+                  is.na(b$PLASER) |
+                  is.na(b$PLASER) & b$FLASER %in% 1:2 |
+                  is.na(b$FLASER) & b$PLASER == 2,
+                  2, 1)

        table(b$pheno, exclude = NULL)

  1   2
859 839

Once again my desired results is to keep these 7 NAs as NAs

table(b$PLASER,b$FLASER, exclude = NULL)

         1   2   3 <NA>
  1    836  14   0    0
  2    691  70  43    2
  3      2   7  21    0
  <NA>   4   1   0    7

and have
825 2s (825=691+14+70+7+43)
and the rest would be 1s (866=1698-7-825)

On Fri, Jun 12, 2020 at 9:29 PM Rasmus Liland <jral at posteo.no> wrote:

On 2020-06-13 11:30 +1000, Jim Lemon wrote:

On Fri, Jun 12, 2020 at 8:06 PM Jim Lemon wrote:

On Sat, Jun 13, 2020 at 10:46 AM Ana Marija wrote:

I am trying to make a new column
"pheno" so that I reduce the number
of NAs

it looks like those two NA values in
PLASER are the ones you want to drop.

From just your summary table, it's hard to
guess the distribution of NA values.

Dear Ana,

This small sample

        b <- read.table(text="FLASER;PLASER
        1;2
        ;2
        ;
        1;
        2;
        2;2
        3;2
        3;3
        1;1", sep=";", header=TRUE)

        table(b$PLASER,b$FLASER, exclude = NULL)

yields the same combinations you showed
earlier:

               1 2 3 <NA>
          1    1 0 0    0
          2    1 1 1    1
          3    0 0 1    0
          <NA> 1 1 0    1

If you want to eliminate the four <NA>-based
combinations completely, this line

        b$pheno <-
          ifelse(b$PLASER==2 |
                 b$FLASER==2 |
                 is.na(b$PLASER) |
                 is.na(b$PLASER) & b$FLASER %in% 1:2 |
                 is.na(b$FLASER) & b$PLASER == 2,
                 2, 1)
        table(b$pheno, exclude = NULL)

will do it:

        1 2
        2 7

Best,
Rasmus