[R] How to remove some rows from a data.frame

[Gabor Grothendieck]

On Dec 23, 2007 4:28 PM, affy snp <affysnp at gmail.com> wrote:
> Hello list,
>
> I have a data frame M like:
>
> BAC                 chr    pos          s1   s2
> RP11-80G24    1    77465510    -1    0
> RP11-198H14    1    78696291    -1    0
> RP11-267M21    1    79681704    -1    0
> RP11-89A19      1    80950808    -1    0
> RP11-6B16        1    82255496    -1    0
> RP11-210E16    1    228801510    0    -1
> RP11-155C15    1    230957584    0    -1
> RP11-210F8      1    237932418    0    -1
> RP11-263L17     2    65724492    0    1
> RP11-340F16     2    65879898    0    1
> RP11-68A1        2    67718674    0    0
> RP11-474G23    2    68318411    0    0
> RP11-218N6      2    68454651    0    0
> CTD-2003M22    2    68567494    0    0
> .....
>
> how to remove those rows which have 0 for both of columns s1,s2?
> sth like M[!M$21=0&!M$s2=0]?
>
> Moreover, I want to get a list which could find a subset of rows which have
> the same pattern of data. For example, the first 8 rows in M can be
> clustered
> into 2 groups (represented below in 2 rows) and shown as:
>
> chr             Start       End             # of rows     Pattern
> 1             77465510   82255496       5              (-1 0)
> 1            228801510  237932418     3              (0 -1)
>

Using:

M <- structure(list(BAC = structure(c(13L, 3L, 8L, 14L, 12L, 4L, 2L,
5L, 7L, 9L, 11L, 10L, 6L, 1L), .Label = c("CTD-2003M22", "RP11-155C15",
"RP11-198H14", "RP11-210E16", "RP11-210F8", "RP11-218N6", "RP11-263L17",
"RP11-267M21", "RP11-340F16", "RP11-474G23", "RP11-68A1", "RP11-6B16",
"RP11-80G24", "RP11-89A19"), class = "factor"), chr = c(1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L), pos = c(77465510L,
78696291L, 79681704L, 80950808L, 82255496L, 228801510L, 230957584L,
237932418L, 65724492L, 65879898L, 67718674L, 68318411L, 68454651L,
68567494L), s1 = c(-1L, -1L, -1L, -1L, -1L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L), s2 = c(0L, 0L, 0L, 0L, 0L, -1L, -1L, -1L, 1L,
1L, 0L, 0L, 0L, 0L)), .Names = c("BAC", "chr", "pos", "s1", "s2"
), class = "data.frame", row.names = c(NA, -14L))

# try this

subset(M, s1 | s2)  # as 0 regarded as FALSE and others as TRUE

# and for second question:

f <- function(x) with(x,
  c(start = pos[1], end = tail(pos, 1),
     chr = chr[1], nrow = NROW(x), s1 = s1[1], s2 = s2[1])
)
do.call(rbind, by(M, M[4:5], f))