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

Tuexy qiuxiaojie1986 at 163.com
Thu Apr 7 15:04:06 CEST 2011

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

#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 =
        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]);

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