#rowdatafix

2018-07-25

Michael Love (16:03:54): > @Michael Love has joined the channel

C. Mirzayi (please do not tag this account) (16:04:34): > @C. Mirzayi (please do not tag this account) has joined the channel

Michael Steinbaugh (16:04:34): > @Michael Steinbaugh has joined the channel

Aedin Culhane (16:04:35): > @Aedin Culhane has joined the channel

Aedin Culhane (16:04:38): > https://community-bioc.slack.com/archives/C6KJHH0M9/p1532123093000148

Ben Johnson (16:04:41): > @Ben Johnson has joined the channel

Matthew McCall (16:04:43): > @Matthew McCall has joined the channel

Aedin Culhane (16:06:22): > Aaron made this comment but I didn’t fully understand -See my previous comments about S4vectors DataFrame name handling changes, and the newuse.names=TRUEdefaulthttps://community-bioc.slack.com/archives/C6KJHH0M9/p1532123159000214

Michael Love (16:08:13): > https://github.com/Bioconductor/SummarizedExperiment/blob/master/inst/unitTests/test_SummarizedExperiment-class.R - Attachment (GitHub): Bioconductor/SummarizedExperiment > SummarizedExperiment container

Michael Steinbaugh (16:09:21): > Okay here’s another SE bug that I came across a while ago and forgot to file

Matthew McCall (16:09:21): > https://github.com/Bioconductor/SummarizedExperiment/blob/9e00e22b5b4456bf2887bbb85daef17bb61f4143/inst/unitTests/test_SummarizedExperiment-class.R#L37 - Attachment (GitHub): Bioconductor/SummarizedExperiment > SummarizedExperiment container

Michael Steinbaugh (16:09:29): > Here’s an example SCE dataset:https://www.dropbox.com/s/eq9g2cjwd5p96mn/sce.rds?dl=1

Michael Steinbaugh (16:10:03): > This is another issue I came across that I’ll try to file on GitHub. > Using an SCE namedscethat hasrowRangesdefined: > > rse <- as(sce, "RangedSummarizedExperiment") > se_has_rowdata <- as(rse, "SummarizedExperiment") > se_null_rowdata <- as(sce, "SummarizedExperiment") >

Simon Coetzee (16:10:14): > @Simon Coetzee has joined the channel

Michael Steinbaugh (16:10:24): > SingleCellExperimentor other classes that extendRangedSumarizedExperimentwill droprowDatawhen coerced directly toSummarizedExperiment

Michael Steinbaugh (16:10:39): > If you go SCE to RSE to SE it works

Michael Love (16:13:15): > rowData(se)vsrowData(se, use.names=TRUE)

Simon Coetzee (16:18:42): > https://github.com/Bioconductor/SummarizedExperiment/commit/4b4f03cd353414bc8a3a76cee150eae8562da9d2 - Attachment (GitHub): feature: rowData() gets use.names = TRUE · Bioconductor/SummarizedExperiment@4b4f03c > - satisfies common use case - changes default behavior - closes #2 ; see also drisso/SingleCellExperiment#16

Aedin Culhane (16:21:14): > > mat <- matrix(rnorm(30), ncol=3) > > rownames(mat) = paste0(“G”, 1:10) > > rowdata = DataFrame(ID = paste0(“G”, 1:10)) > > > > sce = SingleCellExperiment(assays=list(counts=mat), rowData = rowdata) > > rowData(sce) ## note no rownames > DataFrame with 10 rows and 1 column > ID > > 1 G1 > 2 G2 > 3 G3 > 4 G4 > 5 G5 > 6 G6 > 7 G7 > 8 G8 > 9 G9 > 10 G10 > > se = SummarizedExperiment(assays=list(counts=mat), rowData = rowdata) > > rowData(se) ## note rownames > DataFrame with 10 rows and 1 column > ID > > G1 G1 > G2 G2 > G3 G3 > G4 G4 > G5 G5 > G6 G6 > G7 G7 > G8 G8 > G9 G9 > G10 G10 > ```

C. Mirzayi (please do not tag this account) (16:22:11): > I am very new to Bioconductor and so sorry that I am not contributing much but they appear to be discussing the issue here if that’s helpful:https://github.com/Bioconductor/SummarizedExperiment/issues/2 - Attachment (GitHub): rowData does not contain the rownames · Issue #2 · Bioconductor/SummarizedExperiment > library(SummarizedExperiment) example(SummarizedExperiment) rownames(se) <- paste0("Gene", seq_len(nrow(se))) rownames(se)[1:10] ## [1] "Gene1" "Gene2" "Gene3&…

Michael Love (16:30:07): > https://github.com/Bioconductor/SummarizedExperiment/blob/1cf9771ecdacecbedd250fda9606b1809e40c329/R/RangedSummarizedExperiment-class.R#L139-L140 - Attachment (GitHub): Bioconductor/SummarizedExperiment > SummarizedExperiment container

Michael Steinbaugh (16:31:56): > Here’s the assignment method source code:https://github.com/Bioconductor/SummarizedExperiment/blob/1cf9771ecdacecbedd250fda9606b1809e40c329/R/RangedSummarizedExperiment-class.R#L237 - Attachment (GitHub): Bioconductor/SummarizedExperiment > SummarizedExperiment container

Michael Steinbaugh (16:32:07): > SeesetReplaceMethod

Aedin Culhane (16:32:13): > https://github.com/Bioconductor/SummarizedExperiment/blob/1cf9771ecdacecbedd250fda9606b1809e40c329/R/RangedSummarizedExperiment-class.R#L113-L126 - Attachment (GitHub): Bioconductor/SummarizedExperiment > SummarizedExperiment container

Michael Love (16:40:03): > https://gist.github.com/mikelove/8fb94c610b588d4a6a64848d3fcbdf76

Michael Love (16:40:20): > this is a reproducing example