How to analyze count matrix from Synapse.org
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3.9 years ago
yzfmonster ▴ 20

Hi all,

I downloaded this file from Synapse.org, which is a count matrix for RNAseq data. https://www.synapse.org/#!Synapse:syn5053498

I downloaded it to R, and this file is Formal Class File. I do not know how to proceed with this file to analyze the data.

Any help would be appreciated!

RNA-Seq synapse data analysis • 1.2k views
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There is no such thing as a "Formal Class File" in R. I don't want to create an account just to check this file, but it seems a plain text file. How did you load it into R? Depending on the method used, then the resulting object may be of a particular class (instead of being a matrix, for example).

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Hi Thank you for reply.

I downloaded by first installing their interface package called synapseClient. and logged in by synapseLogin.

library(synapseClient)
synapseLogin('login', 'pw', rememberMe = T)

and I use the code below to get the file "syn5053499"

syn5053499 <- synGet(id='syn5053499')
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