remove/replace unwanted character from a column in R

Question

[mthm]

I have a table with an unwanted repeated character in the column5 "Motif:"

xyz.00290   1565    1575    Target   Motif:TART_DV-Dmon-A 743 795   10
xyz.00291   1576    1617    Target   Motif:Maverick-5_Dmon 256 297  41
xyz.00292   1619    1632    Target   Motif:Jockey-18_Dmon 1702 1771 13

I tried to remove it in R; gsub(df, "Motif:", "") but it ruins the whole table by merging all the columns in one!

I also tried str_remove(df, "Motif:") but it does the same.

how should I make them work? and why does it take soooo long for R to run and finish?! is there a faster way around it considering that my files are big (~12000 lines)

[cpad0112]

> df <- data.frame(A="xyz.00290", B="Motif:foo-123")
> df
          A             B
1 xyz.00290 Motif:foo-123
> df$B=stringr::str_split_fixed(df$B,":",2)[2]
> df
          A       B
1 xyz.00290 foo-123

or

> df$B=sub(".*:","",df$B)
> df
          A       B
1 xyz.00290 foo-123

Answer 1

[ATpoint]

Run it on the particular column, not the entire df:

df <- data.frame(A="xyz.00290", B="Motif:foo-123")
> df

         A             B
 xyz.00290 Motif:foo-123

df$B <- gsub("Motif:", "", df$B)

> df
         A       B
 xyz.00290 foo-123

By the way, 12000 rows is in no way big, if simple things like string substitution take more than a second then your command is flawed in most cases.

Answer 2

[Basti]

Look at the documentation of these 2 functions before applying it to an entire data.frame or table :

gsub(pattern, replacement, x, ignore.case = FALSE, perl = FALSE,
     fixed = FALSE, useBytes = FALSE)

x, text : a character vector where matches are sought, or an object which can be coerced by as.character to a character vector. Long vectors are supported.

str_remove(string, pattern)

string : Input vector. Either a character vector, or something coercible to one.

You are applying two functions that require vector as input to a data.frame/table.

Using lapply, you can use these functions :

df[] <- lapply(df, function(x) gsub("Motif:", "", x, fixed = TRUE)) 
df[] <- lapply(df, function(x) str_remove(x, "Motif:"))

[Trivas]

Your explanation of why the OPs code didn't work is great, but this does not need lapply when they can do df$column instead.

[Basti]

Sure but I hoped to provide a general approach if you need to remove a pattern from an entire dataframe and not only a single column