You beat me by one second :D
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Carlo Yague
Lost in "if else" statement R
Hi every body! I'm trying to perform an R loop to processes one of my data frame in which I've stored ChiP seq data. My data frame looks like this
chr1 700245 714068 - 13824 uc001abo.3
chr1 934342 935552 - 1211 uc001aci.2
chr1 1189292 1203372 - 14081 uc001adm.4
chr1 1189292 1209234 - 19943 uc001ado.3
chr1 1243994 1247057 + 3064 uc001aed.3
And I want to handle the 2nd and 3rd columns (adding and subtracting some values). To do that, I've create the code as follow:
import_file= read.delim("file", sep="\t", header = F)
file =as.data.frame.matrix(import_file)
#length( file$V6)
for (i in length file$V6)){
if (any( file$V4 == '-')) {
file$V2 = file$V3-150
file$V3 = file$V3 +50
}
else {
#if file$V4 == '+' do this
file$V2 = file$V2-50
file$V3 = file$V2 +150
}
}
The first "if" statement is processed fine, but for "else", the loop repeat the "if" statement for the other condition. What I want to do is
if (any( file$V4 == '-')) {
file$V2 = file$V3-150
file$V3 = file$V3 +50
#works
and
if file$V4 == '+' do this
file$V2 = file$V2-50
file$V3 = file$V2 +150
#doesn't work
Any help?
Thanks a lot!
4 answers
You're not subsetting file inside your for loop, so if(any(file$V4 == '-')) will always be true. Get rid of the any() and only change the ith entry.
Having said that:
idx = which(file$V4 == '-')
file$V2[idx] = file$V3[idx] - 150
file$V3[idx] = file$V3[idx] +50
idx = which(file$V4 != '-')
file$V2[idx] = file$V2[idx] - 50
file$V3[idx] = file$V2[idx] +150
Alternatively, convert this to a GRanges object and use flank(), which is strand aware.
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Devon Ryan
I typed less, that's why :)
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Devon Ryan
I think you should use [i] in your if/else. Or I don't understand the purpose of that loop.
import_file= read.delim("file", sep="\t", header = F)
file =as.data.frame.matrix(import_file)
#length( file$V6)
for (i in c(1:length(file$V6))){
if (( file$V4 [i]== '-')) {
file$V2[i] = file$V3[i]-150
file$V3[i] = file$V3[i] +50
}
else {
#if file$V4[i] == '+' do this
file$V2[i] = file$V2[i]-50
file$V3[i] = file$V2[i] +150
}
}
PS : indentation is your friend.
PPS : This code could be much more efficient without a loop:
file$V2[which(file$V4=='-')]=file$V3[which(file$V4=='-')]-150
file$V3[which(file$V4=='-')]=file$V3[which(file$V4=='-')]+50
...
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Carlo Yague
Thank you for the advice! The first code that you propose doesn't work at all, the second one is fine for "-" but when I do the same in the "+"
unique_intersect$V2[which(unique_intersect$V4=='+')]=unique_intersect$V2[which(unique_intersect$V4=='+')]-50
unique_intersect$V3[which(unique_intersect$V4=='+')]=unique_intersect$V2[which(unique_intersect$V4=='+')]+150
the result for unique_intersect$V3 is calculated using unique_intersect$V2[which(unique_intersect$V4=='+')]-50 , so the statement doesn't do exactly what I want. Any way, I keep trying!!!
Oh I see, there is a grammatical error (that I copied pasted from your code). for (i in length file$V6)){ should be for (i in c(1:length(file$V6))){. It is now fixed.
Once corrected, the code outputs this : Is it what you want ?
V1 V2 V3 V4 V5 V6
1 chr1 713918 714118 - 13824 uc001abo.3
2 chr1 935402 935602 - 1211 uc001aci.2
3 chr1 1203222 1203422 - 14081 uc001adm.4
4 chr1 1209084 1209284 - 19943 uc001ado.3
5 chr1 1243944 1244094 + 3064 uc001aed.3
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Carlo Yague
I think you can do it by another way:
library(dplyr)
data <- tbl_df(read.table("file_path", header = F, stringsAsFactors = F))
#
data_1 <- filter(data, V4 == "+")
data_1$V2 = data_1$V2-50
data_1$V3 = data_1$V2 +150
#
data_2 <- filter(data, V4 == "-")
data_2$V2 = data_2$V3 - 150
data_2$V3 = data_2$V3 + 50
#
result <- rbind(data_1, data_2)
I haven't done any R for a while but: Are you sure any() is doing what you expect it to do? I just googled it and it says about any, all: 'Check whether any or all of the elements of a vector are TRUE.' This suggest to me that if one line of the vector (=column in your case) is true, the expression returns true. So that behaviour would make perfectly sense (because you aways have a '-' in that column that you posted). So I suggest that you investigate this and I think you have to change your condition a little bit.
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Hi guys, your approaches perform the calculation over the modified data (after adding or subtracting) not over the original data frame (that is exactly what I want) :)
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