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!
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.
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.
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Could you be more specific about what you want to do with those and in which language of programmation ?
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.
It's unclear which data you currently have. Reads? Alignments? Count tables?
Here is the data of miRNA I downloaded. [I updated the image on the topic.]
Or you could be just more informative instead of expecting us to click on anonymous links.
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.