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Issue with Pre-process the data in Monocle3 #17

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anksharm88 opened this issue Apr 18, 2022 · 0 comments
Open

Issue with Pre-process the data in Monocle3 #17

anksharm88 opened this issue Apr 18, 2022 · 0 comments

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@anksharm88
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anksharm88 commented Apr 18, 2022

HI,
I am trying to use monocle on the sample data provided by "https://cole-trapnell-lab.github.io/monocle3/docs/clustering/".

However, at "cds <- preprocess_cds(cds, num_dim = 100)" I am getting the following error.

Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘colVars’ for signature ‘"dgCMatrix"’

My codes are:

library(monocle3)
library(dplyr) # imported for some downstream data manipulation
library(Matrix)
expression_matrix <- readRDS(url("http://staff.washington.edu/hpliner/data/cao_l2_expression.rds"))
cell_metadata <- readRDS(url("http://staff.washington.edu/hpliner/data/cao_l2_colData.rds"))
gene_annotation <- readRDS(url("http://staff.washington.edu/hpliner/data/cao_l2_rowData.rds"))

cds = new_cell_data_set(expression_matrix,
cell_metadata = cell_metadata,
gene_metadata = gene_annotation)
cds <- preprocess_cds(cds, num_dim = 50) # I am getting error at this point

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