Errors when running BayesPrism with gene symbles.

[Sphingosine]

Hi,

I was running BayesPrism using gene symbols and met this error when running functions plot.scRNA.outlier and plot.bulk.outlier:

" Error in input.genes.short %in% gene.df[gene.df[, 1] == gene.group.i, :
object 'input.genes.short' not found "

I found it's due to the function "assign.category" in "process_input.R" and made a very slight change to make it work:
#detect if EMSEMBLE ID (starts with ENS) or gene symbol is used
if( sum(substr(input.genes,1,3)=="ENS")> length(input.genes)*0.8 ){
cat("EMSEMBLE IDs detected.\n")
input.genes.short <- unlist(lapply(input.genes, function(gene.id) strsplit(gene.id,split="\.")[[1]][1]))
gene.df <- gene.list[,c(1,2)]
gene.group.matrix <- do.call(cbind.data.frame, lapply(unique(gene.df[,1]),
function(gene.group.i) input.genes.short %in% gene.df[gene.df[,1]== gene.group.i,2]))
}
else{
cat("Gene symbols detected. Recommend to use EMSEMBLE IDs for more unique mapping.\n")
gene.df <- gene.list[,c(1,3)]
gene.group.matrix <- do.call(cbind.data.frame, lapply(unique(gene.df[,1]),
function(gene.group.i) input.genes %in% gene.df[gene.df[,1]== gene.group.i,2]))
}

Hope it helps : )

Thanks!
Shuai

[tinyi]

Hi Shuai, Thank you very much for your catch. It is fixed now. Best, Tinyi

…

On Wed, Jun 22, 2022 at 4:42 AM SG-ShuaiGuo ***@***.***> wrote: Hi, I was running BayesPrism using gene symbols and met this error when running functions plot.scRNA.outlier and plot.bulk.outlier: " Error in input.genes.short %in% gene.df[gene.df[, 1] == gene.group.i, : object 'input.genes.short' not found " I found it's due to the function "assign.category" in "process_input.R" and made a very slight change to make it work: - #detect if EMSEMBLE ID (starts with ENS) or gene symbol is used - if( sum(substr(input.genes,1,3)=="ENS")> length(input.genes)*0.8 ){ - cat("EMSEMBLE IDs detected.\n") - input.genes.short <- unlist(lapply(input.genes, function(gene.id) strsplit(gene.id,split="\\.")[[1]][1])) - gene.df <- gene.list[,c(1,2)] - gene.group.matrix <- do.call(cbind.data.frame, lapply(unique(gene.df[,1]), - function(gene.group.i) input.genes.short %in% gene.df[gene.df[,1]== gene.group.i,2])) - } - else{ - cat("Gene symbols detected. Recommend to use EMSEMBLE IDs for more unique mapping.\n") - gene.df <- gene.list[,c(1,3)] - gene.group.matrix <- do.call(cbind.data.frame, lapply(unique(gene.df[,1]), - function(gene.group.i) input.genes %in% gene.df[gene.df[,1]== gene.group.i,2])) - } Hope it helps : ) Thanks! Shuai — Reply to this email directly, view it on GitHub <#1>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB4NHSZFJUICEEBUPKLIYUDVQLGYLANCNFSM5ZPL5ZUA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>