[R] add an idx column to the matrix

[Sarah Goslee]

On Wed, Aug 12, 2015 at 2:23 PM, Lida Zeighami <lid.zigh at gmail.com> wrote:
> Thanks Sarah,
>
> I use your code in a loop, so each time I have different matrix, means
> lofGT_met changed each time!
> some times I have just one column in matrix so my matrix will be n*1 (the
> number of rows is the same =n)
> do you think it cause the error?

Not if it is really a two-dimensional object. That's why I suggested
you provide a *reproducible example*.

> onecol <- data.frame(aa=c(1, 2, 3, NA))
> onecol
  aa
1  1
2  2
3  3
4 NA
> apply(onecol, 1, function(x)as.numeric(any(x == 2 & !is.na(x))))
[1] 0 1 0 0

> onecol <- as.vector(onecol[,1])
> onecol
[1]  1  2  3 NA
> apply(onecol, 1, function(x)as.numeric(any(x == 2 & !is.na(x))))
Error in apply(onecol, 1, function(x) as.numeric(any(x == 2 & !is.na(x)))) :
  dim(X) must have a positive length


>
> On Wed, Aug 12, 2015 at 1:12 PM, Sarah Goslee <sarah.goslee at gmail.com>
> wrote:
>>
>> On Wed, Aug 12, 2015 at 2:04 PM, Lida Zeighami <lid.zigh at gmail.com> wrote:
>> > I applied this code in a loop function but since in some matrices there
>> > isn't any 2, so I got the below error:
>> >
>> > idx<- apply(lofGT_met,1, function(x)as.numeric(any(x==2 & !is.na(x))))
>> >
>> >
>> > Error in apply(lofGT_met, 1, function(x){(any(x == 2)}) :
>> >   dim(X) must have a positive length
>>
>> That has nothing to do with whether there are any values of 2 in the
>> data frame. The code I suggested can handle that:
>>
>>
>> no2 <- structure(list(X125 = c(0L, 1L, 1L, 0L, 1L), X255 = c(1L, 1L,
>>  1L, 1L, 0L), X558 = c(0L, 0L, 1L, 0L, 0L), X2366 = c(NA, NA,
>>  1L, NA, 0L), X177 = c(0L, 0L, 0L, 0L, 0L), X255.1 = c(0L, 1L,
>>  0L, 0L, 0L)), .Names = c("X125", "X255", "X558", "X2366", "X177",
>>  "X255.1"), class = "data.frame", row.names = c("aa", "bb", "cs",
>>  "de", "gh"))
>>
>> no2
>> apply(no2, 1, function(x)as.numeric(any(x == 2 & !is.na(x))))
>>
>>
>> > no2
>>    X125 X255 X558 X2366 X177 X255.1
>> aa    0    1    0    NA    0      0
>> bb    1    1    0    NA    0      1
>> cs    1    1    1     1    0      0
>> de    0    1    0    NA    0      0
>> gh    1    0    0     0    0      0
>> > apply(no2, 1, function(x)as.numeric(any(x == 2 & !is.na(x))))
>> aa bb cs de gh
>>  0  0  0  0  0
>>
>> It also works for rows that are entirely NA. Thus, I'm forced to
>> conclude that there's something odd about lofGT_met, and you'll need
>> to provide more information about that data frame, and a reproducible
>> example, for a solution to be offered.
>>
>> Sarah
>>
>>
>> >
>> > would you please let me know how to correct it?
>> > Thanks
>> >
>> > On Mon, Aug 10, 2015 at 3:27 PM, Sarah Goslee <sarah.goslee at gmail.com>
>> > wrote:
>> >>
>> >> Easy enough (note that your column names are problematic, though)
>> >>
>> >> > mydata <- structure(list(X125 = c(0L, 1L, 2L, 0L, 2L), X255 = c(1L,
>> >> > 1L,
>> >> + 1L, 1L, 0L), X558 = c(0L, 0L, 2L, 0L, 0L), X2366 = c(NA, NA,
>> >> + 1L, NA, 0L), X177 = c(0L, 0L, 0L, 0L, 0L), X255.1 = c(0L, 1L,
>> >> + 0L, 0L, 0L)), .Names = c("X125", "X255", "X558", "X2366", "X177",
>> >> + "X255.1"), class = "data.frame", row.names = c("aa", "bb", "cs",
>> >> + "de", "gh"))
>> >> > mydata$idx <- apply(mydata, 1, function(x)as.numeric(any(x == 2 &
>> >> > !is.na(x))))
>> >> > mydata
>> >>    X125 X255 X558 X2366 X177 X255.1 idx
>> >> aa    0    1    0    NA    0      0   0
>> >> bb    1    1    0    NA    0      1   0
>> >> cs    2    1    2     1      0      0   1
>> >> de    0    1    0    NA    0      0   0
>> >> gh    2    0    0     0      0      0   1
>> >>
>> >> Sarah
>> >>
>> >> On Mon, Aug 10, 2015 at 4:11 PM, Lida Zeighami <lid.zigh at gmail.com>
>> >> wrote:
>> >>>
>> >>> Hi there,
>> >>>
>> >>> I have a matrix contain 0,1,2, NA elements.
>> >>> I want to add a column to this matrix with name of "idx" . then for
>> >>> each
>> >>> row, I should put 1 in this column (idx) if there is at least one 2 in
>> >>> that
>> >>> row otherwise I should put 0 in this column!
>> >>>
>> >>> for example  mydata:
>> >>>
>> >>>        125   255   558   2366   177    255
>> >>> aa    0        1       0         NA    0         0
>> >>> bb    1        1       0         NA    0         1
>> >>> cs     2        1       2         1       0         0
>> >>> de    0        1       0         NA    0         0
>> >>> gh    2       0       0         0        0         0
>> >>>
>> >>>
>> >>> my output should be:
>> >>>
>> >>>
>> >>>        125   255   558   2366   177    255    idx
>> >>> aa    0        1       0         NA    0         0      0
>> >>> bb    1        1       0         NA    0         1      0
>> >>> cs     2        1       2         1       0         0     1
>> >>> de    0        1       0         NA    0         0      0
>> >>> gh    2       0       0        2        0         2       1
>> >>>
>
>