coexEnrich

[sunynping]

when i try to run this code ,i get this error could not find function "coexEnrich"???

[pspealman]

Hi - I'm not sure if that is a function in this code.
Can you tell me what command you're running?

[sunynping]

the DEGs Enrichment function&nbsp; ## Perform MEGENA enrichment ```{r} tm.DEG <- NULL for (d in DEGs) {&nbsp; &nbsp; # use DEGs list &nbsp; o <- coexEnrich(y, d, bg) &nbsp; tm.DEG <- cbind(tm.DEG, o) } cp <- apply(tm.DEG[,grep("p.value", colnames(tm.DEG))], 2, as.numeric) #cp <- apply(tm.DEG[,grep("corr.p.val", colnames(tm.DEG))], 2, as.numeric) ix<-apply(cp, 2, function(x) all(is.na(x))) cp <- cp[,which(!ix)]&nbsp; # remove all NA columns if ( is.null(dim(cp))) {next}&nbsp; &nbsp;# one-dim cp colnames(cp) <- names(DEGs)[!ix] rnk <- rankOrder(cp) module <- sub("c1_", "M", tm.DEG[,1]) tmp <- cbind(tm.DEG[,1], module, rnk, cp) # cannot include cp matrix as # of DEGs differ #&nbsp; tm.cp.rank <- rbind(tm.cp.rank, tmp) fn2 <- paste0(tmbase, "_", tID, ".tsv") write.table(tmp, file=fn2, row.names=F, quote=F, sep="\t")

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------------------&nbsp;原始邮件&nbsp;------------------ 发件人: "GreshamLab/RNAseq" ***@***.***&gt;; 发送时间:&nbsp;2023年10月27日(星期五) 中午11:12 ***@***.***&gt;; ***@***.******@***.***&gt;; 主题:&nbsp;Re: [GreshamLab/RNAseq] coexEnrich (Issue #2) Hi - I'm not sure if that is a function in this code. Can you tell me what command you're running? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***&gt;

[pspealman]

I noticed this was a crosspost from CIVR_HRP_Day0.
After checking their code I found the snippet you included.
CIVR_HRP_Day0 is not maintained by me but I have updated their issue with this data and have reached out to the lead to update them.

[sunynping]

Sorry to trouble you,&nbsp;Thanks a million

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------------------&nbsp;原始邮件&nbsp;------------------ 发件人: "GreshamLab/RNAseq" ***@***.***&gt;; 发送时间:&nbsp;2023年10月27日(星期五) 晚上8:57 ***@***.***&gt;; ***@***.******@***.***&gt;; 主题:&nbsp;Re: [GreshamLab/RNAseq] coexEnrich (Issue #2) I noticed this was a crosspost from CIVR_HRP_Day0. After checking their code I found the snippet you included. CIVR_HRP_Day0 is not maintained by me but I have updated their issue with this data and have reached out to the lead to update them. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***&gt;