This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to iterate over all elements of a dataframe and make changes based on a function

I have a dataframe with many cols. Some of the cols have vectors in them. What I want to do, is for everything in the df, if the elements of the vectors are identical, to change the vector to one element but if there is at least one difference, to keep it.

an example of my dataframe:

enter image description here

this is the output that I want

enter image description here

Basically,

> if length(unique(each_vector))==1-> do nothing , otherwise, only choose the first element of the vector.

I would be thankful if someone could help

function r datafram
• 2,628 views • link
written by maria2019 maria2019

I guess first, how did you end up in this situation? Second, are the data frame elements lists, or are they filled with strings like "c(1, 2, 3)"?

• 0 views • link
written by rpolicastro rpolicastro

No, they are not filled with strings. exactly same as the photo that I have posted.

it is the out put of the following code:

df <- aggregate(df, by= list(df$ID) ,FUN='list')
• 0 views • link
written by maria2019 maria2019

Can you add your data to the post with dput(df)?

• 0 views • link
written by rpolicastro rpolicastro 
    dput(df)


"HLA-DRB1*14:05:01", "HLA-DRB1*14:54:01", 
"HLA-DRB1*15:01:01:01", "HLA-DRB1*15:01:01:02", "HLA-DRB1*15:01:01:03", 
"HLA-DRB1*15:01:01:04", "HLA-DRB1*15:02:01", "HLA-DRB1*15:03:01:01", 
"HLA-DRB1*15:03:01:02", "HLA-DRB1*16:02:01"), class = "factor"), 
    start = c(155190174L, 155190174L, 155190174L, 155190174L, 
    155190174L, 155190174L, 155190174L, 155190174L, 155190174L, 
    155190174L, 155190174L), end = c(155190174L, 155190174L, 
    155190174L, 155190174L, 155190174L, 155190174L, 155190174L, 
    155190174L, 155190174L, 155190174L, 155190174L), width = c(1L, 
    1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), strand = structure(c(3L, 
    3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L), .Label = c("+", 
    "-", "*"), class = "factor"), REF = c("C", "C", "C", "C", 
    "C", "C", "C", "C", "C", "C", "C"), ALT = c("G", "G", "G", 
    "G", "G", "G", "G", "G", "G", "G", "G"), FILTER = c("VQSRTrancheSNP99.90to100.00", 
    "VQSRTrancheSNP99.90to100.00", "VQSRTrancheSNP99.90to100.00", 
    "VQSRTrancheSNP99.90to100.00", "VQSRTrancheSNP99.90to100.00", 
    "VQSRTrancheSNP99.90to100.00", "VQSRTrancheSNP99.90to100.00", 
    "VQSRTrancheSNP99.90to100.00", "VQSRTrancheSNP99.90to100.00", 
    "VQSRTrancheSNP99.90to100.00", "VQSRTrancheSNP99.90to100.00"
    ), IMPACT_SnpEff = c("MODIFIER", "MODIFIER", "MODIFIER", 
    "MODIFIER", "MODIFIER", "MODIFIER", "MODIFIER", "MODIFIER", 
    "MODIFIER", "MODIFIER", "MODIFIER"), Feature_SnpEff = c("ENST00000624572.1", 
    "ENST00000624572.1", "ENST00000624572.1", "ENST00000624572.1", 
    "ENST00000624572.1", "ENST00000624572.1", "ENST00000624572.1", 
    "ENST00000624572.1", "ENST00000624572.1", "ENST00000624572.1", 
    "ENST00000624572.1"), Feature_VEP = c("ENST00000467134", 
    "ENST00000468978", "ENST00000471283", "ENST00000473363", 
    "ENST00000485118", "ENST00000498431", "ENST00000610359", 
    "ENST00000610468", "ENST00000611571", "ENST00000611577", 
    "ENST00000612778"), BIOTYPE_SnpEff = c("protein_coding", 
    "protein_coding", "protein_coding", "protein_coding", "protein_coding", 
    "protein_coding", "protein_coding", "protein_coding", "protein_coding", 
    "protein_coding", "protein_coding"), Feature_type_SnpEff = c("transcript", 
    "transcript", "transcript", "transcript", "transcript", "transcript", 
    "transcript", "transcript", "transcript", "transcript", "transcript"
    )), row.names = 290:300, class = "data.frame")

    df_agg<-aggregate(df, by= list(df$Row.names) ,FUN='list') 
    dput(df_agg)


    "HLA-DRB1*14:05:01", "HLA-DRB1*14:54:01", "HLA-DRB1*15:01:01:01", 
    "HLA-DRB1*15:01:01:02", "HLA-DRB1*15:01:01:03", "HLA-DRB1*15:01:01:04", 
    "HLA-DRB1*15:02:01", "HLA-DRB1*15:03:01:01", "HLA-DRB1*15:03:01:02", 
    "HLA-DRB1*16:02:01"), class = "factor")), start = list(c(155190174L, 
155190174L, 155190174L, 155190174L, 155190174L, 155190174L, 155190174L, 
155190174L, 155190174L, 155190174L, 155190174L, 155190174L, 155190174L, 
155190174L, 155190174L, 155190174L, 155190174L, 155190174L, 155190174L, 
155190174L, 155190174L, 155190174L, 155190174L, 155190174L, 155190174L
), c(155190178L, 155190178L, 155190178L, 155190178L, 155190178L, 
155190178L)), end = list(c(155190174L, 155190174L, 155190174L, 
155190174L, 155190174L, 155190174L, 155190174L, 155190174L, 155190174L, 
155190174L, 155190174L, 155190174L, 155190174L, 155190174L, 155190174L, 
155190174L, 155190174L, 155190174L, 155190174L, 155190174L, 155190174L, 
155190174L, 155190174L, 155190174L, 155190174L), c(155190178L, 
155190178L, 155190178L, 155190178L, 155190178L, 155190178L)), 
    width = list(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
    1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), 
        c(1L, 1L, 1L, 1L, 1L, 1L)), strand = list(structure(c(3L, 
    3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 
    3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L), .Label = c("+", "-", 
    "*"), class = "factor"), structure(c(3L, 3L, 3L, 3L, 3L, 
    3L), .Label = c("+", "-", "*"), class = "factor")), REF = list(
        c("C", "C", "C", "C", "C", "C", "C", "C", "C", "C", "C", 
        "C", "C", "C", "C", "C", "C", "C", "C", "C", "C", "C", 
        "C", "C", "C"), c("C", "C", "C", "C", "C", "C")), ALT = list(
        c("G", "G", "G", "G", "G", "G", "G", "G", "G", "G", "G", 
        "G", "G", "G", "G", "G", "G", "G", "G", "G", "G", "G", 
        "G", "G", "G"), c("G", "G", "G", "G", "G", "G")), FILTER = list(
        c("VQSRTrancheSNP99.90to100.00", "VQSRTrancheSNP99.90to100.00", 
        "VQSRTrancheSNP99.90to100.00", "VQSRTrancheSNP99.90to100.00", 
        "VQSRTrancheSNP99.90to100.00", "VQSRTrancheSNP99.90to100.00", 
        "VQSRTrancheSNP99.90to100.00", "VQSRTrancheSNP99.90to100.00", 
        "VQSRTrancheSNP99.90to100.00", "VQSRTrancheSNP99.90to100.00", 
        "VQSRTrancheSNP99.90to100.00", "VQSRTrancheSNP99.90to100.00", 
        "VQSRTrancheSNP99.90to100.00", "VQSRTrancheSNP99.90to100.00", 
        "VQSRTrancheSNP99.90to100.00", "VQSRTrancheSNP99.90to100.00", 
        "VQSRTrancheSNP99.90to100.00", "VQSRTrancheSNP99.90to100.00", 
        "VQSRTrancheSNP99.90to100.00", "VQSRTrancheSNP99.90to100.00", 
        "VQSRTrancheSNP99.90to100.00", "VQSRTrancheSNP99.90to100.00", 
        "VQSRTrancheSNP99.90to100.00", "VQSRTrancheSNP99.90to100.00", 
        "VQSRTrancheSNP99.90to100.00"), c("VQSRTrancheSNP99.90to100.00", 
        "VQSRTrancheSNP99.90to100.00", "VQSRTrancheSNP99.90to100.00", 
        "VQSRTrancheSNP99.90to100.00", "VQSRTrancheSNP99.90to100.00", 
        "VQSRTrancheSNP99.90to100.00")), IMPACT_SnpEff = list(
        c("MODIFIER", "MODIFIER", "MODIFIER", "MODIFIER", "MODIFIER", 
        "MODIFIER", "MODIFIER", "MODIFIER", "MODIFIER", "MODIFIER", 
        "MODIFIER", "MODIFIER", "MODIFIER", "MODIFIER", "MODIFIER", 
        "MODIFIER", "MODIFIER", "MODIFIER", "MODIFIER", "MODIFIER", 
        "MODIFIER", "MODIFIER", "MODIFIER", "MODIFIER", "MODIFIER"
        ), c("MODIFIER", "MODIFIER", "MODIFIER", "MODIFIER", 
        "MODIFIER", "MODIFIER")), Feature_SnpEff = list(c("ENST00000624572.1", 
    "ENST00000624572.1", "ENST00000624572.1", "ENST00000624572.1", 
    "ENST00000624572.1", "ENST00000624572.1", "ENST00000624572.1", 
    "ENST00000624572.1", "ENST00000624572.1", "ENST00000624572.1", 
    "ENST00000624572.1", "ENST00000624572.1", "ENST00000624572.1", 
    "ENST00000624572.1", "ENST00000624572.1", "ENST00000624572.1", 
    "ENST00000624572.1", "ENST00000624572.1", "ENST00000624572.1", 
    "ENST00000624572.1", "ENST00000624572.1", "ENST00000624572.1", 
    "ENST00000624572.1", "ENST00000624572.1", "ENST00000624572.1"
    ), c("ENST00000473363.2", "ENST00000473363.2", "ENST00000473363.2", 
    "ENST00000473363.2", "ENST00000473363.2", "ENST00000473363.2"
    )), Feature_VEP = list(c("ENST00000368392", "ENST00000368393", 
    "ENST00000368396", "ENST00000368398", "ENST00000438413", 
    "ENST00000447623", "ENST00000457295", "ENST00000462215", 
    "ENST00000462317", "ENST00000466913", "ENST00000467134", 
    "ENST00000468978", "ENST00000471283", "ENST00000473363", 
    "ENST00000485118", "ENST00000498431", "ENST00000610359", 
    "ENST00000610468", "ENST00000611571", "ENST00000611577", 
    "ENST00000612778", "ENST00000614519", "ENST00000615517", 
    "ENST00000620103", "ENST00000620770"), c("ENST00000337604", 
    "ENST00000338684", "ENST00000342482", "ENST00000343256", 
    "ENST00000368389", "ENST00000368390")), BIOTYPE_SnpEff = list(
        c("protein_coding", "protein_coding", "protein_coding", 
        "protein_coding", "protein_coding", "protein_coding", 
        "protein_coding", "protein_coding", "protein_coding", 
        "protein_coding", "protein_coding", "protein_coding", 
        "protein_coding", "protein_coding", "protein_coding", 
        "protein_coding", "protein_coding", "protein_coding", 
        "protein_coding", "protein_coding", "protein_coding", 
        "protein_coding", "protein_coding", "protein_coding", 
        "protein_coding"), c("nonsense_mediated_decay", "nonsense_mediated_decay", 
        "nonsense_mediated_decay", "nonsense_mediated_decay", 
        "nonsense_mediated_decay", "nonsense_mediated_decay")), 
    Feature_type_SnpEff = list(c("transcript", "transcript", 
    "transcript", "transcript", "transcript", "transcript", "transcript", 
    "transcript", "transcript", "transcript", "transcript", "transcript", 
    "transcript", "transcript", "transcript", "transcript", "transcript", 
    "transcript", "transcript", "transcript", "transcript", "transcript", 
    "transcript", "transcript", "transcript"), c("transcript", 
    "transcript", "transcript", "transcript", "transcript", "transcript"
    ))), row.names = c(NA, -2L), class = "data.frame")
• 0 views • link
updated by rpolicastro rpolicastro • written by maria2019 maria2019

1 answer

Example data.

df <- structure(list(row = 1:4, col1 = list("X", c("X", "X", "X"), 
    c("X", "X", "Y"), "Y"), col2 = list(c(1, 2), c(1, 1, 1, 1, 
1), 1, c(1, 2, 3))), row.names = c(NA, -4L), class = "data.frame")

> df
  row    col1          col2
1   1       X          1, 2
2   2 X, X, X 1, 1, 1, 1, 1
3   3 X, X, Y             1
4   4       Y       1, 2, 3

base R answer.

check_unique <- \(x) if (length(unique(x)) == 1) unique(x) else x
df[, 2:ncol(df)] <- lapply(df[, 2:ncol(df)], sapply, check_unique)

> df
  row    col1    col2
1   1       X    1, 2
2   2       X       1
3   3 X, X, Y       1
4   4       Y 1, 2, 3
• 0 views • link
written by rpolicastro rpolicastro

thanks for your code

• 0 views • link
written by maria2019 maria2019

Log in to answer this question.

More posts like this