How to iterate over all elements of a dataframe and make changes based on a function
1
0
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2.4 years ago
maria2019 ▴ 250

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 • 1.6k views
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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)"?

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

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    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")
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2.4 years ago

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
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thanks for your code

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