Create gene expression matrix from miRNA
2
0
Entering edit mode
3.9 years ago
landscape95 ▴ 180

I need to create a matrix of miRNA that consists of rows for gene and columns for samples in R. miRNA data is downloaded by TCGAbiolinks.

Your help is really appreciated!

enter image description here

miRNA • 1.4k views
ADD COMMENT
0
Entering edit mode

Could you be more specific about what you want to do with those and in which language of programmation ?

ADD REPLY
0
Entering edit mode

I use R programming language. I want to create a correlation network and for further usage. Here is the data of miRNA I downloaded. I update the image on the topic.

ADD REPLY
0
Entering edit mode

It's unclear which data you currently have. Reads? Alignments? Count tables?

ADD REPLY
0
Entering edit mode

Here is the data of miRNA I downloaded. [I updated the image on the topic.]

ADD REPLY
1
Entering edit mode

Or you could be just more informative instead of expecting us to click on anonymous links.

ADD REPLY
0
Entering edit mode

Yes, I am sorry. To be more specific. I want to express via the image. I updated the image on the topic. Hope you can see it.

ADD REPLY
2
Entering edit mode
3.9 years ago
h.mon 32k

Did you read this data into R? This is a pretty basic operation. Did you have a look at the data? Do you know which columns you want / need to use for your analysis? See the R helps for:

?read.delim

?read.table

And search for "subset data frame R" on your favorite search engine.

ADD COMMENT
2
Entering edit mode
3.9 years ago
VHahaut ★ 1.1k

It doesn't really tell us for what is it but here is a code in R to get the count data into a matrix:

  • Assuming that this is in a text file (and not excel) that is located on your desktop at this address: "~/Desktop/count.txt"

    a <- read.table("~/Desktop/count.txt", header=T, row.names=1, sep="\t")

    a <- as.matrix(a[,grep("read_count", colnames(a))])

This should probably work.

ADD COMMENT

Login before adding your answer.

Traffic: 1954 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6