Easiest way to convert read10xMolInfo data into a dataframe in R with gene labels as row names
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Sitapriya • 0
@4f700f46
Last seen 11 weeks ago
United States

Hi, I have been playing around with the read10xMolInfo.

What I am looking for is a simple solution wherein I can convert the .h5 file into an R data frame or data table and have gene names added as a separate columns or as row names.

I came up with this solution but wondering if this works?

I am assuming here that the genes are indexed.

Meaning: Gene ID in position 1 (in the gene list) corresponds to the gene ID labels = 1 in the mol.info table.

mol.info <- read10xMolInfo(mol.info.file.h5)

mol.info.df <- mol.info$data %>% data.frame()

molecule.df.gene.name <- mol.info.df%>% 
    mutate(Gene = mol.info$genes[gene])
tidyverse R SingleCellExperiment SingleCellData • 331 views
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Initially posted to https://github.com/MarioniLab/DropletUtils/issues/104 geometry dash scratch

Thanks for sharing this link. I also have the same problem

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Peter Hickey ▴ 670
@petehaitch
Last seen 21 hours ago
WEHI, Melbourne, Australia

An example usually helps. Here's a way to do it using base R.

library(DropletUtils)

# Mocking up some 10X HDF5-formatted data.
out <- DropletUtils:::simBasicMolInfo(tempfile())

# Reading the resulting file.
mol_info <- read10xMolInfo(out)

# Converting to data.frame.
mol_info_df <- as.data.frame(mol_info$data)
# Replace number in gene column with name.
mol_info_df$gene <- mol_info$gene[mol_info_df$gene]

# View the first few rows of the result.
head(mol_info_df)
#>   cell    umi gem_group   gene reads
#> 1 CCGA 366381         1  ENSG5    13
#> 2 CACG 673390         1  ENSG4     3
#> 3 ACAC 894928         1 ENSG11    10
#> 4 TACG 456777         1 ENSG10    12
#> 5 GATG 757426         1 ENSG14    10
#> 6 GTCT 833839         1  ENSG9    12
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