search for: rpkm

...y the same. My understanding is that rbind takes column names from the first file it reads. However, my output is showing that the column names are treated as a first data row, not treated as headers. I compile my file names like this: > all.files <- list.files() > all.files [1] "1.rpkm" "10.rpkm" "11.rpkm" "12.rpkm" "13.rpkm" "14.rpkm" [7] "15.rpkm" "16.rpkm" "17.rpkm" "18.rpkm" "19.rpkm" "2.rpkm" [13] "3.rpkm" "4.rpkm" "5.rpkm" &q...

...the first file >> it reads. However, my output is showing that the column names are >> treated as a first data row, not treated as headers. >> >> I compile my file names like this: >> >>> all.files <- list.files() >>> all.files >> [1] "1.rpkm" "10.rpkm" "11.rpkm" "12.rpkm" "13.rpkm" "14.rpkm" >> [7] "15.rpkm" "16.rpkm" "17.rpkm" "18.rpkm" "19.rpkm" "2.rpkm" >> [13] "3.rpkm" "4.rpkm" "...

Dear R users, I am running the following code below, the gem751be.rpkm is a dataframe with dim of 751 samples by 35164 variables, 73 phenotypic variables in the furst to 73rd column and 35091 genomic variables or genes in the 74th to 35164th columns. What I need to do is to calculate the residuals for each gene using the simple linear regression model of genelist[i]...

...case anyone else has this question: I boxplotted my y variable data, but did the "cut" operation on the x variable in order to conserve the order of the y data. I see another suggestion coming in from another user that basically says this. So, my working line of code was: boxplot(count$RPKM ~ cut(count$C_count, breaks=4) Much appreciation to everyone who responded...thanks for helping with a na?ve question without making me feel stupid. This discussion board is very, very good. --Kelly V. -----Original Message----- From: David Winsemius [mailto:dwinsemius at comcast.net] Sent: Fr...

...g to build the package: Error: processing vignette ?BitSeq.Rnw' failed with diagnostics: Failed to locate the ?weave? output file (by engine ?utils::Sweave?) for vignette with name ?BitSeq?. The following files exists in directory ?.?: ?data-C0.est?, ?data-C1.est?, ?data-c0b0.prob?, ?data-c0b0.rpkm?, ?data-c0b0.sam?, ?data-c0b0.thetaMeans?, ?data-c0b1.rpkm?, ?data-c1b0.rpkm?, ?data-c1b1.rpkm?, ?data.estVar?, ?data.means?, ?data.par?, ?data.pplr?, ?data.tr?, ?ensSelect1.fasta?, ?ensSelect1.tr?, ?parameters1.txt? Execution halted My guess is it's looking for BitSeq.tex, but it's not cl...

...es, then making a box plot of the relationship between the GeneDensity parameter and each of the three "ReadCount" columns. Here's an example of one of my boxplot commands: boxplot(GeneDensity$ReadCount_Explant ~ cut(GeneDensitySorted$GeneDensity, breaks=10), ylim=c(0,40), ylab="RPKM", xlab="GENE DENSITY (LOW -> HIGH)", main="INTERNODE EXPLANT") Right now, I'm making three separate graphs: one for each of the three "ReadCount" columns. I'd like to put all three sets on one graph, so that each decile is represented by three boxes,...

Hi all, I have been struggling with this problem for a few days. I have a data table like this: gene rpkm1 diff1 rpkm2 diff2 gene1 23 50 13 120 gene2 111 220 827 1200 gene3 75 998 71 910 And I want to re-format it so that, for each gene, I have a 2x2 contingency table, such as: gene rpkm diff gene1 23 50 gene1 13 120 gene2 111 220 gene2 827 1200 gene3 75 998...

...plot of the relationship between the GeneDensity parameter and each of the three "ReadCount" columns. Here's an example of one of my boxplot commands: > > boxplot(GeneDensity$ReadCount_Explant ~ > cut(GeneDensitySorted$GeneDensity, breaks=10), ylim=c(0,40), > ylab="RPKM", xlab="GENE DENSITY (LOW -> HIGH)", main="INTERNODE > EXPLANT") > > Right now, I'm making three separate graphs: one for each of the three "ReadCount" columns. I'd like to put all three sets on one graph, so that each decile is represented by...

...quot; column and the function transforms each such subset of the data.frame into a new data.frame that is just 1 row / transcript that basically has the sum of the "counts" for each transcript. The code would look something like this (`summaries` is the data.frame I'm referring to): rpkm <- ddply(summaries, .(transcript), function(df) { data.frame(symbol=df$symbol[1], counts=sum(df$counts)) } (It actually calculates 2 more columns that are returned in the data.frame, but I'm not sure that's really important here). To test some things out, I've written another fun...

Hi, R-help, I have a group of data from RNA-seq want to be analyzed by Fisher's exact test in R. I want to compare the significant difference of about 30,0000 individuals in two different samples, and I have no idea how to use R, so could you please give me some suggestions or the scripts for Fisher's exact test? Thank you very much. Best, Guanfeng Wang [[alternative HTML version