summarize doesn't work with weighted mean

[UnkindPartition]

library(plyranges)

set.seed(2018)
n <- 10
r <- GRanges(seqnames = rep("chr1", n),
                  ranges = IRanges(start = sample(20, n, replace = T),
                                   width = sample(6,  n, replace = T))
                  )
mcols(r) <- data.frame(score = runif(n, 0, 100), condition = rep_len(c("One","Two"), n))
r

## GRanges object with 10 ranges and 2 metadata columns:
##        seqnames    ranges strand |            score condition
##           <Rle> <IRanges>  <Rle> |        <numeric>  <factor>
##    [1]     chr1       7-9      * | 26.0100793326274       One
##    [2]     chr1     10-13      * | 56.8360368022695       Two
##    [3]     chr1       2-7      * | 15.1498265331611       One
##    [4]     chr1       4-8      * | 9.49368453584611       Two
##    [5]     chr1     10-14      * |  76.191659620963       One
##    [6]     chr1      7-10      * | 53.5928548080847       Two
##    [7]     chr1     13-14      * | 32.7880936674774       One
##    [8]     chr1       3-6      * | 92.4356027971953       Two
##    [9]     chr1     20-24      * | 59.8311740672216       One
##   [10]     chr1     11-15      * | 6.46366507280618       Two
##   -------
##   seqinfo: 1 sequence from an unspecified genome; no seqlengths

These work:

r %>% group_by(condition) %>% summarize(score = mean(score))

## DataFrame with 2 rows and 2 columns
##   condition            score
##    <factor>        <numeric>
## 1       One 41.9941666442901
## 2       Two 43.7643688032404

r %>% group_by(condition) %>% summarize(score = mean(width))

## DataFrame with 2 rows and 2 columns
##   condition     score
##    <factor> <numeric>
## 1       One       4.2
## 2       Two       4.4

r %>% group_by(condition) %>% reduce_ranges(score = weighted.mean(score, width))

## GRanges object with 3 ranges and 2 metadata columns:
##       seqnames    ranges strand | condition            score
##          <Rle> <IRanges>  <Rle> |  <factor>        <numeric>
##   [1]     chr1      2-14      * |       One 38.4664801647887
##   [2]     chr1     20-24      * |       One 59.8311740672216
##   [3]     chr1      3-15      * |       Two 40.5111238942482
##   -------
##   seqinfo: 1 sequence from an unspecified genome; no seqlengths

... but this doesn't:

r %>% group_by(condition) %>% summarize(score = weighted.mean(score, width))

## Error in as.vector(x, mode): coercing an AtomicList object to an atomic vector is supported only for
##   objects with top-level elements of length <= 1

sessionInfo()

## R version 3.5.0 (2018-04-23)
## Platform: x86_64-redhat-linux-gnu (64-bit)
## Running under: Fedora 28 (Workstation Edition)
## 
## Matrix products: default
## BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so
## 
## locale:
##  [1] LC_CTYPE=ru_RU.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_DK.UTF-8        LC_COLLATE=ru_RU.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats4    parallel  stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
## [1] knitr_1.20           rtracklayer_1.40.3   plyranges_1.1.6     
## [4] GenomicRanges_1.32.3 GenomeInfoDb_1.16.0  IRanges_2.14.10     
## [7] S4Vectors_0.18.2     BiocGenerics_0.26.0 
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_0.12.17                pillar_1.2.3               
##  [3] BiocInstaller_1.30.0        compiler_3.5.0             
##  [5] git2r_0.21.0                XVector_0.20.0             
##  [7] bindr_0.1.1                 bitops_1.0-6               
##  [9] tools_3.5.0                 zlibbioc_1.26.0            
## [11] digest_0.6.15               evaluate_0.10.1            
## [13] tibble_1.4.2                memoise_1.1.0              
## [15] lattice_0.20-35             pkgconfig_2.0.1            
## [17] rlang_0.2.1                 Matrix_1.2-14              
## [19] DelayedArray_0.6.0          curl_3.2                   
## [21] yaml_2.1.19                 bindrcpp_0.2.2             
## [23] GenomeInfoDbData_1.1.0      stringr_1.3.1              
## [25] withr_2.1.2                 httr_1.3.1                 
## [27] dplyr_0.7.5                 Biostrings_2.48.0          
## [29] devtools_1.13.5             tidyselect_0.2.4           
## [31] grid_3.5.0                  glue_1.2.0                 
## [33] Biobase_2.40.0              R6_2.2.2                   
## [35] XML_3.98-1.11               BiocParallel_1.14.1        
## [37] tidyr_0.8.1                 purrr_0.2.4                
## [39] magrittr_1.5                Rsamtools_1.32.0           
## [41] matrixStats_0.53.1          GenomicAlignments_1.16.0   
## [43] assertthat_0.2.0            SummarizedExperiment_1.10.1
## [45] stringi_1.2.2               RCurl_1.95-4.10

[sa-lee]

This is to do with some issues we've been talking about in #30 - I need to handle the case when there is not "fast" method for dispatching the grouped object better.

@lawremi I'm surprised there is no List method for weighted.mean?

[lawremi]

This is a limitation in the stats package that I will try to fix. But for now it's a good use case for the fallback to looping.

[sa-lee]

This should be fixed in more recent versions. The more general issue is discussed in #74