Extracting Gene List From Model/Graphs

Analysis
1

Hello!

I am using mixOmics to integrate RNAseq (10K genes) , ATACseq (10K genes), and Protein (8K proteins) data:

I wanted to see various results from my data with inputting the top 10% (about 2,700 from ~28,000 total genes) about 450 for the (Comp1,Comp2) for each dataset. (lol, maybe not the best strategy, but hey… its exploration)…

list.keepX <-list(rna = c(450,450), atac = c(450,450), prot = c(450,450))

result_ten_percent ← block.splsda(X = data_list, Y = response_vector, design = design, keepX = list.keepX)

For the keepX, I just selected 450 genes from comp1 and comp2 for each dataset (900total), and I am assuming it is selecting the top 450 out of the model for each dataset, which should be 2,700 genes. I’d like to submit these genes in a list for pathway analysis in another program.

I would like to extract the gene lists that are show in in the plots? I’m not sure the best way to go about extracting them.

I have purchased the textbook, and if there are instruction is in there, could you direct me to the page. I’ve read most, but perhaps I missed it?

Thanks in advance

plots
plots1920×1038 128 KB

2

hi @DawnL,

Thanks for sharing your results.

To get the list from your block.splsda object, use the function selectVar(result_ten_percent) (look at the arguments, you can specify a specific component).

For the plots (the information will be the same as higher, but sometimes a bit more organised), save each plot into an object then object$... will extract some information (also look at the help file for each plot in the section called Value.

Kim-Anh

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