search for: gene_names

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(S...

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"

...6 Zcwpw1 5 Zdhhc18 6 Zdhhc20 5 Zdhhc3 11 Zeb2 15 The only way I can figure out to do this is via rowsum: > rowsum (Number,Gene_Name) gives me exactly what I want, *except* that in the end, I am left with a matrix containing the Number values and with the Gene_Names used as row names (the output therefore looks exactly as printed above) -- what I want is a dataframe equivalent to the starting table, with numbered rows and separate, accessible columns containing the Gene_Name and Number values. I was able to put such a dataframe together manually, by cobbl...

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 hav...

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

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

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

Hi everyone, I am new to R-project. I did search through the list for my problem but i can't find it. I am sorry if this question has been asked. 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

Hi, r-community, This morning, I MET the following problem several times when I try to attach the data set. When I closed the current console and reopen 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

I do have a bunch of genes ( nearly ~50000) from the whole genome, which read in genomic ranges A range(gene) can be seem as an observation has three columns chromosome, start and end, like that seqnames start end width strand gene1 chr1 1 5 5 + gene2 chr1 10 15 6 + gene3 chr1 12 17 6 + gene4 chr1 20 25 6 + gene5

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