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waldronlab / SingleCellMultiModal

Single Cell multimodal data scripts for downloading datasets
https://bioconductor.org/packages/SingleCellMultiModal
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scNMT: invalid name for slot of class "ExperimentHub": dataType #22

Closed aljabadi closed 4 years ago

aljabadi commented 4 years ago

@LiNk-NY trying to re-load the scNMT-seq data I get:

library(SingleCellMultiModal)
#> Loading required package: MultiAssayExperiment
#> Loading required package: SummarizedExperiment
#> Loading required package: MatrixGenerics
#> Loading required package: matrixStats
#> 
#> Attaching package: 'MatrixGenerics'
#> The following objects are masked from 'package:matrixStats':
#> 
#>     colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
#>     colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
#>     colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
#>     colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
#>     colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
#>     colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
#>     colWeightedMeans, colWeightedMedians, colWeightedSds,
#>     colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
#>     rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
#>     rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
#>     rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
#>     rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
#>     rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
#>     rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
#>     rowWeightedSds, rowWeightedVars
#> Loading required package: GenomicRanges
#> 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, colnames,
#>     dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
#>     grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
#>     order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
#>     rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
#>     union, unique, unsplit, which.max, which.min
#> Loading required package: S4Vectors
#> 
#> Attaching package: 'S4Vectors'
#> The following object is masked from 'package:base':
#> 
#>     expand.grid
#> Loading required package: IRanges
#> Loading required package: GenomeInfoDb
#> 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")'.
#> 
#> Attaching package: 'Biobase'
#> The following object is masked from 'package:MatrixGenerics':
#> 
#>     rowMedians
#> The following objects are masked from 'package:matrixStats':
#> 
#>     anyMissing, rowMedians
gastru.mae <- scNMT(dataType = 'mouse_gastrulation', modes = '*', version = '2.0.0', dry.run = FALSE)
#> Error in initialize(value, ...): invalid name for slot of class "ExperimentHub": dataType

Looking down the stack the problem seems to be caused by passing a dataType arg to ExperimentHub constructor:

new('ExperimentHub', dataType='dataType')
#>  invalid name for slot of class "ExperimentHub": dataType

I looked at ?ExperimentHub-class but unfortunately didn’t see any straightforward clarification as to what this class actually expects in threedots.

Created on 2020-11-27 by the reprex package (v0.3.0)

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LiNk-NY commented 4 years ago

Hi Al, @ajabadi Thanks for reporting this! I will look into it today. -Marcel

LiNk-NY commented 4 years ago

Hi Al, @ajabadi

I had a look at this and it appears that dataType should be DataType in the function call. We can run a check for all the arguments in the call (since we do collect the arguments) and provide a more helpful error message but it seems to me that this would be "too clever".

Let me know if this helps! Best, Marcel

aljabadi commented 4 years ago

Hi Marcel, @LiNk-NY

Thanks for the quick reply and sorry for this trivial oversight. I thought this code had worked in the past but I guess I had misspelled and never had it checked.

I agree, that sort of error catching for a function that takes ... would in fact be too clever :).

Best, Al

LiNk-NY commented 4 years ago

It's not your fault. I remember now that I changed the case in the argument to match the metadata some time ago before the release. :sweat_smile: https://github.com/waldronlab/SingleCellMultiModal/commit/907274e86ce61995002e96836a569c4a73cd72de