condiments Package

[Nab14]

Hi Hector, I have a problem trying to reproduce this part of the code on my data df$scores <- sce[, df$X1]$scores$scaled_scores

I'm getting this error Error in .Primitive("[")(new("dgCMatrix", i = c(8L, 13L, 26L, 28L, 29L, : invalid or not-yet-implemented 'Matrix' subsetting

What X1 stand for? especially that in the next part of the code it replaced by "Cells" Thanks

[HectorRDB]

Could you point me to where this is happening? Which vignette are you refering?

[Nab14]

I was trying to run the KRAS vignette https://hectorrdb.github.io/condimentsPaper/articles/KRAS.html Thank you for your help,

[HectorRDB]

Oh I see, Yes the code is not optimal. It is pulling data from the original study (using the condimentsPaper::import_KRAS function) which does not have a column for cell names per say, so that column is named X1 by default in R. I only rename it later in the vignette as you noted.

As per your error, I think you were using an old version, the correct line should read

df$scores <- kras[, df$X1]$scores$scaled_scores

If you yourself replaced kras with sce, could you please tell me the output of

is(sce)

[Nab14]

I'm using my own data. I used Seurat for clustering and created a sce from a Seurat object Below is the output of is (sce) Thank you

[1] "SingleCellExperiment" "RangedSummarizedExperiment" "SummarizedExperiment" "RectangularData" "Vector"
[6] "Annotated" "vector_OR_Vector"

[HectorRDB]

And how did you create the the df object?

[Nab14]

after imbalance_score ex: sce<- imbalance_score(Object = sce, conditions = "group", dimred = "TSNE")

I used bind_cols then to generate df

df <- bind_cols( as.data.frame(reducedDims(sce)$TSNE), as.data.frame(colData(sce)[, -3]) ) %>% sample_frac(1)

thank you

[HectorRDB]

I see. Is there a column in df that refers to cell names. If so (let's call if cells) you can just do

df$scores <- sce[, df$cells]$scores$scaled_scores

Let me know if taht work

[Nab14]

It's still gives me an error, see below Error in SummarizedExperiment:::.SummarizedExperiment.charbound(subset, : index out of bounds: ATCCACCCACAAATCC-1_2 TCCCAGTTCTCAACGA-1_2 ... GACCGTGGTACGTAGG-1_3 TTACCATTCATTCCTA-1_3

[HectorRDB]

The column you use should match the colnames(sce)

mean(colnames(sce) %in% df$cells) == 1

mean(df$cells %in% colnames(sce)) == 1

Must be true both times Le mar. 25 oct. 2022 à 18:21, Nab14 @.***> a écrit :

It's still gives me an error, see below Error in SummarizedExperiment:::.SummarizedExperiment.charbound(subset, : index out of bounds: ATCCACCCACAAATCC-1_2 TCCCAGTTCTCAACGA-1_2 ... GACCGTGGTACGTAGG-1_3 TTACCATTCATTCCTA-1_3

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[Nab14]

I was able to fix the issue by using the code below Thank you for your help,

df <- df %>% as.data.frame() %>% mutate(cells = rownames(.), conditions = df$group) scores <- imbalance_score(Object = df %>% select(tSNE_1, tSNE_2) %>% as.matrix(), conditions = df$conditions) df$scores <- scores$scaled_scores