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)
2 answers
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.
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:"))
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