Hello,
I have a table in R which consists of 70k rows and 37 columns. Lot of cells have "./." which I want to modify and make it as "ab" . I tried to use gsub() but it does not give me the required output.
I used :
file <- gsub("./.","ab",file)
I want the change to happen throughout the file. Is there any other way with which I can modify it? Thanks in advance.
Input: Eg:
S.no chr pos gene_name S1 S2 S3
1 1 1290 X ./. 1/1 ./.
2 1 5822 Y 0/1 ./. ./.
Output
S.no chr pos gene_name S1 S2 S3
1 1 1290 X ab 1/1 ab
2 1 5822 Y 0/1 ab ab
It can be either ab or NA
•
written
by
Inquisitive8995
Try to use fixed match:
file <- gsub("./.","ab",file, fixed = TRUE)
Or
file[ file == "./." ] <- "ab"
Edit: Using example data provided by OP.
# example input data
df1 <- read.table(text = "
S.no chr pos gene_name S1 S2 S3
1 1 1290 X ./. 1/1 ./.
2 1 5822 Y 0/1 ./. ./.", header = TRUE, stringsAsFactors = FALSE)
df1
# S.no chr pos gene_name S1 S2 S3
# 1 1 1 1290 X ab 1/1 ab
# 2 2 1 5822 Y 0/1 ab ab
df1[, c("S1", "S2", "S3")][ df1[, c("S1", "S2", "S3")] == "./." ] <- "ab"
df1
# S.no chr pos gene_name S1 S2 S3
# 1 1 1 1290 X ab 1/1 ab
# 2 2 1 5822 Y 0/1 ab ab
Thanks for your answer. The second one worked but it does not show "ab" instead it is blank and has "NA"s
df1=read.csv("test.txt", header = T, strip.white = T, stringsAsFactors = F, sep = "\t")
library(stringr)
library(dplyr)
> df1 %>% mutate_all(funs(str_replace_all(.,"\\.[/|\\|]\\.","ab")))
S.no chr pos gene_name S1 S2 S3
1 1 1 1290 X ab 1/1 ab
2 2 1 5822 Y 0/1 ab ab
You can also use apply function:
> library(stringr)
> apply(df1,2, function(x) str_replace_all(x,"\\.[/|\\|]\\.","ab"))
S.no chr pos gene_name S1 S2 S3
[1,] "1" "1" "1290" "X" "ab" "1/1" "ab"
[2,] "2" "1" "5822" "Y" "0/1" "ab" "ab"
This is supposed to replace both ./. and .|.. test.txt is OP input text.
I want only the ./. to be modified not the 1/1.
oops..typo. It doesn't replace any character other than . (./. or .|.). Edited OP. Inquisitive8995
df[df=="./."] = "ab" will do the job, where df is the dataframe of your data
Sorry, somehow missed your solution! Deleting
Log in to answer this question.
Try with
d <- c("./.","./x","x/yy","./.","./.")example, gsub won't work.that was an example code without all corner cases. For the example code posted above, following would work:
I understand . is a regex for any single character (in general). Since OP hasn't provided any data, I used simple case.