[R] Two questions about metacharacter in regexprs and function return

From: Tuexy <qiuxiaojie1986_at_163.com>
Date: Thu, 07 Apr 2011 00:46:26 -0700 (PDT)


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;

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Received on Thu 07 Apr 2011 - 07:58:28 GMT

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