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asmagen / robustSingleCell

Robust single cell clustering and comparison of population compositions across tissues and experimental models via similarity analysis.
http://dx.doi.org/10.1016/j.celrep.2019.10.131
MIT License
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Failing to read data after changing input parameter #7

Closed asmagen closed 5 years ago

asmagen commented 5 years ago

Running initialize.project followed by:

LCMV1 <- setup_LCMV_example()
data.path <- system.file("extdata/LCMV1_small.txt", package = "robustSingleCell")
raw_LCMV1 <- as.matrix(read.table(data.path, check.names = FALSE))

LCMV1 <- read.data(LCMV1,
                   raw.data.matrices = list(LCMV1 = raw_LCMV1),
                   min.genes.per.cell = 100,
                   max.genes.per.cell.quantile = 1,
                   max.UMIs.per.cell.quantile = 1,
                   min.cells.per.gene = 1,
                   rerun = T)

fails with the error:

Error in dimnames(x) <- dn : 
  length of 'dimnames' [2] not equal to array extent
Mamie commented 5 years ago

environment$datasets were modified by read.data, which causes rerun to fail when assigning column names to measurements. Fixed by adding a new attribute dataset_ids to store the information.