[R] seqinr ?: Splitting a factor name into several columns. Dealing with metabarcoding data.

[Ista Zahn]

Hi Anna,


On Sun, Oct 12, 2014 at 3:24 AM, Anna Zakrisson Braeunlich
<anna.zakrisson at su.se> wrote:
> Hi,
>
> I have a question how to split a factor name into different columns. I have metabarcoding data and need to merge the FASTA-file with the taxonomy- and counttable files (dataframes). To be able to do this merge, I need to isolate the common identifier, that unfortunately is baked in with a lot of other labels in the factor name eg:
> sequence identifier: M01271_77_000000000.A8J0P_1_1101_10150_1525.1.322519.sample_1.sample_2
>
> I want to split this name at every "." to get several columns:
> column1: M01271_77_000000000
> column2: A8J0P_1_1101_10150_1525
> column3: 1
> column4: 322519
> column5: sample_1
> column6: sample_2
>
> I must add that I have no influence on how these names are given. This is how thay are supplied from Illumina Miseq. I just need to be able to deal with it.
>
> Here is some extremely simplified dummy data to further show the issue at hand:
>
> df1 <- data.frame(cbind(X = 1:10, Y = rnorm(10)),
>                   Z.identifierA.B1298712 = factor(rep(LETTERS[1:2], each = 5)))
> df2 <- data.frame(cbind(B = 13:22, K = rnorm(10)),
>                   Q.identifierA.B4668726 = factor(rep(LETTERS[1:2], each = 5)))
>
> # I have metabarcoding data with one FASTA-file, one count table and one taxonomy file
> # Above dummy data is just showing the issue at hand. I want to be able to merge my three
> # original data frames (here, the dummy data is only two dataframes). The problem is that
> # the only identifier that is commmon for the dataframes is "hidden" in the
> # factor name eg: Z.identifierA.1298712 and Q.identifierA.4668726. I hence need to be able
> # to split this name up into different columns to get "identifierA" alone as one column name
> # Then I can merge the dataframes.
> # How can I do this in R. I know that it can be done in excel, but I would like to
> # produce a complete R-script to get a fast pipeline and avoid copy and paste errors.
> # This is what I want it to look:
>
> df1.goal <- data.frame(cbind(X = 1:10, Y = rnorm(10)),
>                   Z = factor(rep(LETTERS[1:2], each = 5)),
>                   identifierA = factor(rep(LETTERS[1:2], each = 5)),
>                   B1298712 = factor(rep(LETTERS[1:2], each = 5)))

Use strsplit to separate the components, something like

separateNames <- strsplit(names(df1)[3], split = "\\.")[[1]]
for(name in separateNames) {
    df1[[name]] <- df1[[3]]
}
df1[[3]] <- NULL

Best,
Ista

>
> # Many thank's and with kind regards
> Anna Zakrisson
>
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>
> Anna Zakrisson Braeunlich
> PhD student
>
> Department of Ecology, Environment and Plant Sciences
> Stockholm University
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