search for: gene_name

I am getting an error message, which I do not know the source to. I have a matrix SAMPLES that has preexisting rownames that I would like to change. GENE_NAMES contains these rownames. > rownames(SAMPLES) = GENE_NAMES Error in "dimnames<-.data.frame"(`*tmp*`, value = list(list(V1 = c(3843, : invalid 'dimnames' given for data frame > dim(SAMPLES) [1] 12626 20 > dim(GENE_NAMES) [1] 12626 1 > is.data.frame(...

Dear Experienced R users, I have a looks-like simple but complicated problem urgently needed to be solved. Below is the detail: I have two dataframes, df1, df2. df1 contains two column and many thousands rows: column 1 is a "gene_name", column 2 is "value". df2 contains only one column which is "gene_name" with couple hundred rows. I want to change "value" of df2 for those "gene_name" also appear in df2 "gene_name". How to do that? Millions thanks. Ste

Hi-- This is a question with a trivial and obvious answer, I'm sure, but I can't seem to find it in the help files and books that I have handy. I have a dataframe consisting of two columns, "Gene_Name," a list of gene symbols, and "Number," a numeric measure of how frequently a tag representing that gene showed up in a SAGE library. Several of the genes are represented by multiple tags, and therefore are present more than once in the list, e.g.: 1167 Zcchc8 6 1168 Z...

Any ideas about the following problem: I have a matrix (A) that looks like this: gene_names values hsa-mir-124 0.3 hsa-mir-234 0.1 hsa-mir-344 0.4 hsa-mir-333 0.7 ..... ....... (This is a 2 by 22283 matrix: quite large) I would like to plot the values, but output the gene_names as the plotting symbol. I ha...

HI, Dear R community, My original file has 1932 lines, but when I read into R, it changed to 1068 lines, how comes? cdu@nuuk:~/operon$ wc -l id_name_gh5.txt 1932 id_name_gh5.txt > gene_name<-read.table("/home/cdu/operon/id_name_gh5.txt", sep="\t", skip=0, header=F, fill=T) > dim(gene_name) [1] 1068 3 -- Sincerely, Changbin -- Changbin Du DOE Joint Genome Institute Bldg 400 Rm 457 2800 Mitchell Dr Walnut Creet, CA 94598 Phone: 925-927-2856 [[alternati...

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 ...

Hi, I have the following data file to be parsed and captured as a data frame: __DATA__ #GDS_ID GENE_NAME GENE_DESCRIPTION GENE_FUNCTION 1007_s_at | DDR1 | discoidin domain receptor tyrosine kinase 1 | protein-coding 1053_at | RFC2 | replication factor C (activator 1) 2, 40kDa | protein-coding 117_at | HSPA6 | heat shock 70kDa protein 6 (HSP70B') | protein-coding __END__ In particular it is separ...

...I would like to perform a correlation analysis between a hiv data and gene expression. Basically, i have a file that contains: hiv_name, start_position, end_position, chromosome. I would like to see if these data has anything to do with the location of our genes (I also have another file contains gene_name, start_position, end_position, chromosome). What functions that allow me to do this? I am very new to R and hopefully someone can guide me to the right direction. Thank you very much, [[alternative HTML version deleted]]

...pen the R console, the problem disappear. BUt with the time passed on, the problem occurs again. Can anyone help me with this? > attach(total) The following object(s) are masked from total ( position 3 ) : acid base cell_evalue cell_hit charged freq_cell freq_hypo freq_intra gene_id gene_name hydrophobic hypo_evalue hypo_hit log_cell log_hypo log_pfam num_cell num_genes operon_id outcome pfam_align pfam_evalue pfam_per_id polar position target total_length -- Sincerely, Changbin -- [[alternative HTML version deleted]]

...ne4 chr1 20 25 6 + gene5 chr1 30 40 11 + I just wondering is there an efficient way to find *overlapped, upstream and downstream genes for each gene in the granges* For example, assuming all_genes_gr is a ~50000 genes genomic range, the result I want like belows: gene_name upstream_gene downstream_gene overlapped_gene gene1 NA gene2 NA gene2 gene1 gene4 gene3 gene3 gene1 gene4 gene2 gene4 gene3 gene5 NA Currently , the strategy I use is like that, library(GenomicRanges) find_overlapped_gene <- function(idx, all_genes_gr) { #cat(idx, "\n") curr_ge...

Hi, I have the following data frame: > print(mydatframe) __DATAFRAME__ V1 V2 V3 1 1007_s_at DDR1 discoidin domain receptor tyrosine kinase 1 2 1053_at RFC2 replication factor C (activator 1) 2, 40kDa 3 117_at HSPA6 heat shock 70kDa protein 6 (HSP70B') __END__ Is there a way to create a hash with V2 as Key and V3 as its value? - Gundala Viswanath Jakarta - Indonesia