r - How to rearrange data frame so that values in one column are row names? -


this question has answer here:

i have data frame containing 450k methylation beta-values approx. 450 probes 2 samples. data displayed in 3 columns, , looks this:

>head(icgc)  submitted_sample_id    probe_id    methylation_value 1  x932-01-4d          cg00000029         0.6 2  x932-01-6d          cg00000029         0.4 3  x932-01-4d          cg00000108         0.3 4  x932-01-6d          cg00000108         0.7 5  x932-01-4d          cg00000109         0.9 6  x932-01-6d          cg00000109         0.1

i rearrange data.frame probe ids rownames , sample ids column names, looks this:

>head(icgc_2)            x932-01-4d    x932-01-6d  cg00000029    0.6           0.4 cg00000108    0.3           0.7 cg00000109    0.9           0.1

i have tried:

>library(tidyverse) icgc_2 <- icgc %>% remove_rownames %>% column_to_rownames(var = "probe_id")

but didn't work each probe id in icgc appears twice in column (as there 2 samples). tried:

hello <- data.frame(icgc[,-2], row.names = icgc[,2])

but had same problem. reason want rearrange data in way because convert beta values m-values , use data object in cpg.annotate (available through bioconductor package dmrcate) - cpg.annotate requires object have unique illumina probe ids rownames , unique sample ids column names.

thank you!

you close. spread funciton tidyr package need. 

library(tidyverse)  icgc_2 <- icgc %>%   spread(submitted_sample_id, methylation_value) %>%   remove_rownames() %>%   column_to_rownames(var = "probe_id") icgc_2            x932-01-4d x932-01-6d cg00000029        0.6        0.4 cg00000108        0.3        0.7 cg00000109        0.9        0.1

data:

icgc <- read.table(text = "submitted_sample_id    probe_id    methylation_value 1  'x932-01-4d'          cg00000029         0.6 2  'x932-01-6d'          cg00000029         0.4 3  'x932-01-4d'          cg00000108         0.3 4  'x932-01-6d'          cg00000108         0.7 5  'x932-01-4d'          cg00000109         0.9 6  'x932-01-6d'          cg00000109         0.1",                    header = true, stringsasfactors = false)

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