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JinmiaoChenLab / Batch-effect-removal-benchmarking

A benchmark of batch-effect correction methods for single-cell RNA sequencing data
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true up and down genes missing from simulated data #2

Open rlittman16 opened 4 years ago

rlittman16 commented 4 years ago

Hello,

I was hoping to use your simulated data, but wanted to also have a look at what the true up and down regulated genes are. I saw there was a file created by your splatter script, but the files are missing from the simulation data directories.

Thanks!

nhuhoa commented 4 years ago

Dear rlittman,

The true up-, down- regulated genes info are noted in geneinfo.txt file, the column DEFacGroup. There are 2 groups, so have 2 column: DEFacGroup1, and DEFacGroup2. 1 is not differentially expressed, > 1 is differentially expressed. If I well remember, ex: geneinfo$DEFacGroup1 > 1 mean up-regulated in group 1, down-regulated in group2. More info you can see in Spatter tutorial, the part gene information: https://www.bioconductor.org/packages/release/bioc/vignettes/splatter/inst/doc/splatter.html

If you don't see the simulated data in github folder, you can simply use the provided Splatter script to generate the data, then use heatmap to visualize the deg genes in DEFacGroup1, DEFacGroup2 columns. Good luck!

Get all up-, down-regulated genes: geneinfo <- read.table(paste0('data/',simu,'/geneinfo.txt'), head=T) real_de_genes_ls <- rownames(geneinfo[(geneinfo$DEFacGroup1+geneinfo$DEFacGroup2)!=2,]) deg_gene_ls <- geneinfo[real_de_genes_ls,]

Best, Hoa Tran