Question: How to analyze count matrix from Synapse.org
0
gravatar for yzfmonster
12 months ago by
yzfmonster20
yzfmonster20 wrote:

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 data analysis synapse • 382 views
ADD COMMENTlink written 12 months ago by yzfmonster20

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).

ADD REPLYlink written 12 months ago by h.mon21k

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')
ADD REPLYlink modified 12 months ago • written 12 months ago by yzfmonster20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 571 users visited in the last hour