Hi Martin et al.
When I use "mcols" on a SummerizedExperiment object, I get a DataFrame
with the row metadata, but without rownames. This is quite annoying if I
want to select specific rows using my feature identifiers.
Would it be possible to change that?
Simon
Demonstration of the issue:
> library( GenomicRanges )
[...]
>
> # Example data matrix with row and column names:
> a <- matrix( rnorm(50), c( 10, 5 ) )
> colnames(a) <- paste0( "Sample_", 1:5 )
> rownames(a) <- paste0( "Gene_", sample( LETTERS, 10 ) )
> a
Sample_1 Sample_2 Sample_3 Sample_4 Sample_5
Gene_G -0.3877467 -1.70879454 0.7939223 -2.34550441 0.8595643
Gene_K -0.2552112 0.08670308 -1.4158207 0.66415623 -2.3311998
Gene_M -0.4514518 0.30546322 -0.1799235 1.32129088 0.5253143
Gene_T 0.7403792 0.22984996 0.1972806 1.67471472 0.7371430
Gene_Z 1.0290360 -0.49934034 2.5813815 0.60148770 0.3925438
Gene_B -0.6196811 -0.23720962 1.6226878 -0.39416017 -0.9792215
Gene_W 0.6341272 0.70582774 0.8372586 2.20678476 -1.5472927
Gene_L 0.4160801 -0.60180955 0.5366517 -2.41960274 -0.1754423
Gene_U 1.1331233 0.19707903 -1.1297945 0.03272385 -2.6627403
Gene_A -0.9800668 -0.61572952 -1.4320614 0.16594756 -1.4636233
>
> # Create a SummerizedExperiment from it:
> se <- SummarizedExperiment( a )
>
> # The row names have been taken over from 'a' to 'se':
> rownames(se)
[1] "Gene_G" "Gene_K" "Gene_M" "Gene_T" "Gene_Z" "Gene_B" "Gene_W" "Gene_L"
[9] "Gene_U" "Gene_A"
>
> # Add some meta data:
> mcols(se)$yellowness <- runif(10)
> mcols(se)$greenness <- runif(10)
>
> # Look at the meta data
> mcols(se)
DataFrame with 10 rows and 2 columns
yellowness greenness
<numeric> <numeric>
1 0.0772510 0.77249283
2 0.9760104 0.01193128
3 0.8420076 0.61835914
4 0.2859476 0.97866574
5 0.8153054 0.91518594
6 0.4111647 0.06934432
7 0.9445907 0.39559884
8 0.7793326 0.58575488
9 0.4379305 0.53325324
10 0.2076865 0.46240856
>
> # No row names :-(
>
>
> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] GenomicRanges_1.14.4 XVector_0.2.0 IRanges_1.20.6
[4] BiocGenerics_0.8.0
loaded via a namespace (and not attached):
[1] stats4_3.0.2
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