Check that using list work

[llrs]

I got a strange error about a list not being character. I was using mclusterGeneSim perhaps it was using the function for GeneSetCollection.

The input was:

set.seed(456)
# info
library("reactome.db")
#> Loading required package: AnnotationDbi
#> Loading required package: stats4
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, sd, var, xtabs
#> The following objects are masked from 'package:base':
#> 
#>     anyDuplicated, append, as.data.frame, basename, cbind,
#>     colMeans, colnames, colSums, dirname, do.call, duplicated,
#>     eval, evalq, Filter, Find, get, grep, grepl, intersect,
#>     is.unsorted, lapply, lengths, Map, mapply, match, mget, order,
#>     paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,
#>     Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort,
#>     table, tapply, union, unique, unsplit, which, which.max,
#>     which.min
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> Loading required package: IRanges
#> Loading required package: S4Vectors
#> 
#> Attaching package: 'S4Vectors'
#> The following object is masked from 'package:base':
#> 
#>     expand.grid
library("BioCor")
#> If you use BioCor in published research, please cite:
genes2Pathways <- as.list(reactomeEXTID2PATHID)
pathways <- unlist(genes2Pathways, use.names = FALSE)
genes <- rep(names(genes2Pathways), lengths(genes2Pathways))
paths2genes <- split(genes, pathways)
human <- grep("R-HSA-", names(paths2genes))
paths2genes <- paths2genes[human]
paths2genes <- lapply(paths2genes, unique)
paths2genes <- paths2genes[lengths(paths2genes) >= 2]
genes2paths <- GSEAdv:::inverseList(paths2genes)

# clusters
clusters <- list(a=sample(genes, 50), b = sample(genes, 25))
mclusterGeneSim(clusters, info = genes2paths, method = c("max", "BMA"))
#> Warning in mclusterGeneSim(clusters, info = genes2paths, method =
#> c("max", : Some genes are not in the list provided.
#> Error in if (is.na(rowIds) || is.na(colIds)) {: missing value where TRUE/FALSE needed
mclusterGeneSim(clusters, info = paths2genes, method = c("max", "BMA"))
#> Warning in mclusterGeneSim(clusters, info = paths2genes, method =
#> c("max", : Some genes are not in the list provided.
#> Error in mpathSim(pathwaysl, info, NULL): The input pathways should be characters

^{Created on 2018-11-15 by the reprex package (v0.2.1)}

[llrs]

In an unexpected turn of the events using GeneSetCollections doesn't work!!

gsc <- GSEAdv::as.GeneSetCollection(genes2paths)
o3 <- mclusterSim(clusters, info = gsc, method = "max")
#> Error in keep[keep] : invalid subscript type 'list'
gsc2 <- GSEAdv::as.GeneSetCollection(paths2genes)
o3 <- mclusterSim(clusters, info = gsc2, method = "max")
#> Warning message:
#> In mclusterSim(clusters, info = gsc2, method = "max") :
#>   At least one gene should be in the GeneSetCollection provided

As if the expected gsc is the other way around, genes and the pathways names!!

[llrs]

In the server the above code works, so it might be something of the installation on this specific machine

[llrs]

The first bug about a missing value is related to getting NULL, so I added a check for NULL in the conditions (Although I should explore more)

The second error was due to using unique(keepPaths[keepPaths]) instead of any(keepPaths) as it does now. It produces an incorrect subseting of the lists