ESTIMATE tumor purity

Question

[JACKY]

Hello, I'm searching for a way to calculate the ESTIMATE tumor purity, using genes expression matrix. I found something close, https://github.com/mwsill/RFpurify

However this doesn't seem suitable for RNA-seq data, is was trained on methylation array data.

Any suggestions for such a package in R?

[JACKY]

Anyone? I'm kinda in trouble and realy could use some help with this package. I've used many packages in my life but this is by far the most peculiar one..

Answer 1

[JACKY]

Just in case anyone faces this problem in the future, here is the link for the updated estimate package on github:

https://github.com/KaiAragaki/tidyestimate

for some reason this package is hidden. After days of searching I have finally found it.

Answer 2

[fracarb8]

ESTIMATE is an R package that, quoting the authors, calculates scores for tumor purity, the level of stromal cells present, and the infiltration level of immune cells in tumor tissues based on expression data.

install.packages("estimate", repos="http://r-forge.r-project.org", dependencies=TRUE) will get you started.

[JACKY]

Thank you fracarb8 ! I've seen this package before I just read somewhere it's not fit for RNA-seq, but turns out they were wrong it does work for RNA-seq.

Anyone, I couldn't find any user guide for this package, do you know of any guide I could use? Their website is not much informative in that matter.

In the R help for this package, there is this code: platform = c("affymetrix", "agilent", "illumina")) , what platform is suitable for RNA-seq? is it illumina?

[fracarb8]

The website suggests you to run help(package="estimate") to get the documentation.

[JACKY]

It doesn't specify how can it be done for RNA-seq, all the exmaples are for microarray..