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BaderLab / Tempora

Pathway-based trajectory inference method for time-series scRNAseq data
MIT License
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Problem with IdentifyVaryingPWs #8

Closed DustinSokolowski closed 4 years ago

DustinSokolowski commented 4 years ago

Hello!

When running the Tempora workflow, we found an error in the IdentifyVaryingPWs function. In the for loop on line 41, there is no option for when themes[i] is not in rownames(gsva_bycluster) (or length(grep(themes[i], rownames(gsva_bycluster))) == 0).

I remade the function locally and added: the following code which helped: if(length(grep(themes[i], rownames(gsva_bycluster))) == 0) { p_vals[[i]] <- 1 gams[[i]] <- "no_gam_available" next }

Best! Dustin

DustinSokolowski commented 4 years ago

oops if(length(grep(themes[i], rownames(gsva_bycluster))) == 0) { p_vals[[i]] <- 1 gams[[i]] <- "no_gam_available" next }

thinh-tran commented 4 years ago

Hi Dustin! Thanks for bringing this to my attention and sorry for the late response. I have fixed the loop now as suggested.