Change format of counts of single cell RNA-seq data from csv to mtx format from synapse.org

Question

[ali_karimnezhad]

I have downloaded a count matrix of a single-cell dataset in csv format (let's call it a.csv) from synaps.org, with the following structure:

i j x
34 1 1
35 1 1
43 1 1
74 1 1

How can I generate the corresponding count matrix in R in mtx format? I have two meta data file associated with a.csv. Here I provide the first two lines of those files (with modifications)

b.csv:

    cell_name    specimenID     broad_class      subtype
1   cellname1    specimenID1    Exc              Exc.Exc.L3
2   cellname2    specimenID2    Exc              Exc.Exc.L3

c.csv:

X    x
1    gene1
2    gene2

[Ram]

Please put effort into formatting your post better. See this post for tips: How to Use Biostars Part-3: Formatting Text and Using GitHub Gists

I've fixed your post this time.

[ali_karimnezhad]

Thank you Ram

[ATpoint]

Isn't that already mtx format? Try to read that first csv with `Matrix::readMM` into R and see what happens. The other two files are then the row- and coldata to annotate that matrix. You probably want to make a more suitable format to work downstream, e.g. SingleCellExperiment or Seurat. Does that make sense?

[ali_karimnezhad]

Thanks for your reply ATpoint .

No, unfortunately, it is not in mtx format. readMM gives the following error:

file is not a MatrixMarket file

Answer 1

[ali_karimnezhad]

I was finally able to solve the issue. Here is the code I used:

library(data.table)
synapser::synLogin()
counts <- fread(synapser::synGet('syn23554292')$path )  # this reads the a.csv file
i=as.vector(counts$i)
j=as.vector(counts$j)
x=as.vector(counts$x)
library(Matrix)
A <- sparseMatrix(i, j, x)                 
Meta.cells <- read.csv(synapser::synGet('syn23554294')$path, header=T, stringsAsFactors = F) # this reads the b.csv file
Meta.genes <- read.csv(synapser::synGet('syn23554293')$path, header=T, stringsAsFactors = F ) # this reads the c.csv file
rownames(A)=Meta.genes$x
colnames(A)=Meta.cells$cell_name