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IMB-Computational-Genomics-Lab / ascend

R package - Analysis of Single Cell Expression, Normalisation and Differential expression (ascend)
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"Please ensure 'counts' are in your supplied assay list" #25

Closed daacarri closed 5 years ago

daacarri commented 5 years ago

Hello,

I am trying to create a new EmSET from a single cell object. I keep getting an error in which it says I need to ensure 'counts' are in supplied assay list. However, when I check the structure of this single cell object, my assay is indeed listed as counts... Not sure why it isn't recognizing this? I have tried many different permutations but can't seem to get this to work.

asenabouth commented 5 years ago

Hi @daacarri ,

Thank you for reporting this issue. I'll see if I can replicate this and get back to you on a fix.

daacarri commented 5 years ago

Here is an example of the scripts I used:

matrix_dir = "path" barcodes.path <- paste0(matrix_dir, "barcodes.tsv") genes.path <- paste0(matrix_dir, "genes.tsv") matrix.path <- paste0(matrix_dir, "matrix.mtx") mat <- readMM(file = matrix.path) genes.names = read.delim(genes.path, header = FALSE, stringsAsFactors = FALSE) barcodes.names = read.delim(barcodes.path, header = FALSE, stringsAsFactors = FALSE) colnames(mat) = barcodes.names$V1 rownames(mat) = genes.names$V2

example <- SingleCellExperiment(assays = list(counts = mat), #create single cell object colData = barcodes.names, rowData = genes.names$V2)

em_set_example <- newEMSet(example) Error in newEMSet(example) : Please ensure 'counts' are in your supplied assay list.

asenabouth commented 5 years ago

Hi @daacarri ,

I will need some time to fix the class conversion. In the meantime, you can create an EMSet by using your single cell data directly. You can use the loadCellRanger(path) function which will generate the object for you.

Anne

asenabouth commented 5 years ago

Hi @daacarri , Issue should be fixed with the latest update. Please let me know if there's still an issue.