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jmanitz / kangar00

development of kangar00
https://cran.r-project.org/package=kangar00
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warning msg in pathway_info('hsa04020') #25

Closed jmanitz closed 6 years ago

jmanitz commented 6 years ago

pathway_info('hsa04020') # warning msg: In pathway_info("hsa04020") : NAs introduced by coercion

source:

info$chromosome_name <- as.numeric(as.character(info$chromosome_name)) Warning message: NAs introduced by coercion

jmanitz commented 6 years ago

code simplified and fixed:

info <- stats::na.omit(getBM(attributes=c("start_position","end_position", "chromosome_name","hgnc_symbol"), filters=c("hgnc_symbol"), values=g, mart=ensembl)) pathways <- data.frame(pathway=x, info)

before: info$chromosome_name <- as.numeric(info$chromosome_name) info <- stats::na.omit(info) pathways <- cbind(rep(paste(x,sep=""),length(info[,1])),info)