for the script, please kindly see the script below. At line 10 and line 13, my problems occurs. The first one is I try to retrieve the gene official name from a column of a table. The pattern of official name is something starting with gene_name. For detail problems, please see the according lines. Any suggestions are appreciated
example of matching source (extract the Nnat, sometime it would be the character "N/A"): "AB004048|MM8;NCBI Build 36|transcript|chr2|157251580|157253958|ExemplarFor 'AB004048'; gene_id '18111'; transcript_id 'AB004048'; gene_name 'Nnat'; alt '5730414I02Rik|AW107673|Peg5'; neuronatin|http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=full_report&list_uids=18111"; #obtain the exprs matrix for cluster analysis #ask questions DEG_files <- grep("bak", dir());#pay attention to the filenames exprs_files <- grep("copy", dir()); protein <- c(); assign_exprs <- function(files, protein) { #use to find the DEGs or exprs for cmeans clustering for(i in 1:length(files)) { microarray_data <- read.csv(file = files[i], header = T, sep = "\t"); microarray_data[, 7] <- gsub("([\\s\\S]+gene_name '(\\w*)';.+)", "\\2", microarray_data[, 7], perl = T);#why [\\w]* cannot workable? also the [(\\w*)(N/A)] cannot be workable. assign(files[i], microarray_data, envir=.GlobalEnv); #get(dir()[i]() can obtain the data of interest.`variable_names` can also work protein <- c(protein, get(files[i])[, 7]); #used for obtain all the DEGs only } #return protein; #why this line is not workable? assign("all_protein", protein, envir=.GlobalEnv); } exist_to_cluster_exprs <- function(x, cluster_exprs, all) { if(exists("all", x[1])){ #exists function cluster_exprs <- cbind(cluster_exprs, x); } #return cluster_exprs; } assign_exprs(dir()[DEG_files], protein); all_protein <- unique(all_protein); assign_exprs(dir()[exprs_files], protein); for(i in 1:2) { apply(get(dir()[exprs_files[i]]), 1, exist_to_cluster_exprs, cluster_exprs, all); #assign(paste(exprs_files()[i], "exprs_data"), cluster_exprs[, c(2, 3, 5, 7)]; exprs_data <- cbind(exprs_data, cluster_exprs[, 3]); } exprs_data; -- View this message in context: http://r.789695.n4.nabble.com/Two-questions-about-metacharacter-in-regexprs-and-function-return-tp3433342p3433342.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
