On Jul 9, 2011, at 4:38 PM, David Winsemius wrote:
On Jul 9, 2011, at 12:45 PM, Bansal, Vikas wrote:
Dear sir,
I was doing with different code that is why u did not get output
which I was saying.Please use this code on summary file-
I have a file that is summary.txt(I have attached it) .we can read
this file using-
dfa=read.table("summar.txt",fill=T,colClasses = "character",header=T)
In V10 column I have ASCII values which I converted into decimal
numbers using this code-
dfa$V10 <- sapply(dfa$V10, function(a)
paste(as.integer(charToRaw(a)), collapse = ' '))
now you will get this output.
dfa
V7 V8 V9 V10
1 0 1 G 96
snipped
26 0 1 C 95
27 0 1 A 88
28 0 1 g 96
29 0 2 GG 92 92
30 0 2 GG 91 94
31 0 2 AT 89 94
32 0 2 GG 96 93
the values in column V10 corresponds to A,C,G T in column V9.I want
only those, whose score is more than 90.so output of above should be-
V7 V8 V9 V10
1 0 1 G 96
snipped the easy lines
29 0 2 GG 92 92
30 0 2 GG 91 94
31 0 2 T 89 94
32 0 2 GG 96 93
so in output 15th and 27th row should be deleted and 31st row
should be-
31 0 2 T 89 94
because 89 is score for A and 94 is score for T.Therefore A has
been deleted because its score is less than 90.
At the moment I have a version of dfa that has the original V10 and
another column named 'value' in the fifth position. Since apply
removes attributes and names, functions written to work with an
apply function need to refer to positions:
I'm not sure where I picked up that incorrect notion. You could use
x["V9"] where I typed x[3] and c["value" where I typed x[5].
dfa$newcol <-
apply(dfa, 1, function(x){ # create index vectors for letters in V9
vals <- c( sapply(strsplit(x[5], " "), as.numeric))
# use paste to make them into single character string
# so they will fit back into a dataframe
paste( unlist(
# # unlist the list of qualifying letters in third column and
strsplit(x[3],"")[ which(vals >=90)] ),
collapse=" ")} )
And since I want to correct a big error up above, I will mention that
I used collapse=", " for this output:
Here's the middle of that dataframe:
> dfa
V7 V8 V9 V10 value newcol
snipped
25 0 1 A a 97 A
26 0 1 C _ 95 C
27 0 1 A X 88
28 0 1 g ` 96 g
29 0 2 GG \\\\ 92 92 G, G
30 0 2 GG [^ 91 94 G, G
31 0 2 AA Y^ 89 94 A
32 0 2 GG `] 96 93 G, G
33 0 2 AA a^ 97 94 A, A
34 0 2 GG ]^ 93 94 G, G
35 0 2 AA a\\ 97 92 A, A
36 0 2 GG a] 97 93 G, G
37 0 2 GG Z] 90 93 G, G
38 0 2 GG ]^ 93 94 G, G
39 0 2 CC W\\ 87 92 C
40 0 2 CC a] 97 93 C, C
41 0 2 TT `` 96 96 T, T
42 0 2 GG a\\ 97 92 G, G
43 0 2 GG `` 96 96 G, G
44 0 2 aa aa 97 97 a, a
45 0 2 AA a^ 97 94 A, A
46 0 2 CC b` 98 96 C, C
47 0 2 AA _\\ 95 92 A, A
48 0 2 CC ]` 93 96 C, C
49 0 2 TT ^\\ 94 92 T, T
50 0 2 CC Z` 90 96 C, C
51 0 2 Ac `a 96 97 A, c
52 0 3 AAA b`a 98 96 97 A, A, A
53 0 3 GGG aa] 97 97 93 G, G, G
snipped -- getting way too long
David Winsemius, MD
West Hartford, CT
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