I have a variation on the oh-so-common problem of how to merge things together in R.
I have a set of .txt files in a particular folder, and I have written a function that:
What I end up with is a list with the following structure:
>str(DataList)
List of 16
$ :'data.frame': 14 obs. of 2 variables:
..$ Sample: Factor w/ 14 levels "Sample_1A","Sample_1B",..: 1 2 3 4 5 6 7 8 9 10 ...
..$ Var1 : num [1:14] 27.9 33.8 29.9 29.4 28.8 ...
$ :'data.frame': 14 obs. of 2 variables:
..$ Sample: Factor w/ 14 levels "Sample_1A","Sample_1B",..: 1 2 3 4 5 6 7 8 9 10 ...
..$ Var2 : num [1:14] 24.6 27 26.8 26.7 27.2 ...
$ :'data.frame': 12 obs. of 2 variables:
..$ Sample: Factor w/ 14 levels "Sample_1A","Sample_1B",..: 1 2 3 4 5 6 7 9 11 12 ...
..$ Var3 : num [1:12] 31.4 35.6 34 35.7 32.5 ...
For each variable (Var1, Var2, Var3,
...) I have a column Sample
and a column of numerical values.
Sample
is always a factor with 14 levels; these levels are the same for each variable.
The problem is that some variables (like Var3
above) don't have observations for each level of Sample
.
What I want to end up with is a data frame with 14 rows (one for each level of Sample
). The first column should be Sample
; then for each variable, there should be a column containing the corresponding numerical values, like so:
Sample Var1 Var2 Var3
Sample_1A 27.9 24.6 31.4
Sample_1B 33.8 27 35.6
...
Sample_3B 26.8 29.7 NA
I've been trying to do this with do.call
, but don't know how to pass the arguments for by
; cbind
gets unhappy because of the missing values. Any thoughts on how to do this?
Thanks!
EDIT: As per joran's request:
>dput(DataList[1:3])
list(structure(list(Sample = structure(1:14, .Label = c("Sample_1B", "Sample_1C", "Sample_1D", "Sample_2C", "Sample_2A", "Sample_2D", "Sample_3B", "Sample_3C", "Sample_3A", "Sample_3D", "Sample_4B", "Sample_4C", "Sample_4A", "Sample_4D"), class = "factor"), Var1 = c(26.9333333333333, 29.17, 28.9366666666667, 28.9233333333333, 28.61, 28.63, 26.7933333333333, 34.6633333333333, 30.4966666666667, 28.4433333333333, 27.4533333333333, 28.3, 27.9633333333333, 27.2366666666667)), .Names = c("Sample", "Var1"), row.names = c(NA, -14L), class = "data.frame"), structure(list(Sample = structure(1:14, .Label = c("Sample_1B", "Sample_1C", "Sample_1D", "Sample_2C", "Sample_2A", "Sample_2D", "Sample_3B", "Sample_3C", "Sample_3A", "Sample_3D", "Sample_4B", "Sample_4C", "Sample_4A", "Sample_4D"), class = "factor"), Var2 = c(24.19, 26.6033333333333, 26.0366666666667, 27.6766666666667, 27.61, 27.5633333333333, 25.1566666666667, 33.7266666666667, 27.7, 26.1466666666667, 25.65, 26.3633333333333, 25.5333333333333, 26.1733333333333)), .Names = c("Sample", "Var2"), row.names = c(NA, -14L), class = "data.frame"), structure(list(Sample = structure(c(1L, 2L, 3L, 4L, 5L, 6L, 7L, 9L, 11L, 12L, 13L, 14L), .Label = c("Sample_1B", "Sample_1C", "Sample_1D", "Sample_2C", "Sample_2A", "Sample_2D", "Sample_3B", "Sample_3C", "Sample_3A", "Sample_3D", "Sample_4B", "Sample_4C", "Sample_4A", "Sample_4D"), class = "factor"), Var3 = c(31.4133333333333, 35.56, 33.9666666666667, 35.66, 32.4633333333333, 31.99, 31.3133333333333, 36.34, 34.9433333333333, 34.5433333333333, 34.3766666666667, 33.28)), .Names = c("Sample", "Var3"), row.names = c(NA, -12L), class = "data.frame"))
Looks like a textbook use case for Reduce
.
merge.all <- function(x, y) {
merge(x, y, all=TRUE, by="Sample")
}
output <- Reduce(merge.all, DataList)
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