The question about installing manually

[WortJohn]

When i install PopSV manually and the command is " install.packages('./PopSV-master.zip', repos=NULL)", the error that is "Error in rawToChar(block[seq_len(ns)]) : The nul embeds into string : 'PK\003\004\n\0\0\0\0\0O\177\x86J\0\0\0\0\0\0\0\0\0\0\0\0\r\0\t\0PopSV-master/UT\005\0\001\026\xc8\xe6XPK\003\004\n\0\0\0\b\0O\177\x86J@\036\xdc/\030\0\0\0\032\0\0\0\027\0\t\0PopSV-master/.giti' " arises.

I don't have permission to install it through install_github, so i install it manually. But the error arises, please help me. Thank you!

[jmonlong]

To install manually with this command, you have to unzip PopSV-master.zip first and use the command on the unzipped folder, e.g. install.packages('./PopSV-master', repos=NULL).

In theory you shouldn't need permissions to install a package (in your home). If the issue with install_github is something about certificates, then you may be able to install PopSV directly using devtools::install_git("http://github.com/jmonlong/PopSV.git"). This is an error I encountered in some computing clusters and the newest R versions.

Let me know if you have more troubles.

[WortJohn]

@jmonlong Thanks for your helps firstly. I already install it successfully. But when i load it like "library(PopSV)", the warning message that is "replacing previous import by ‘data.table::shift’ when loading ‘PopSV’" arises. I don't care it at first. But when i want to use the "fdrtool.quantile" function, the error whic is "no have the function" arises. Use it like your "fdr = fdrtool.quantile(z.df$z,quant.int=seq(.6,.99,.01))" from test-mergeBins.R. Is there some influence bewteen them?

[jmonlong]

Sorry for the late response. The function fdrtool.quantile is an internal function and you don't have to call it directly. The example you found is a unit test used to be sure that the package performs correctly, but not something that you should try to reproduce.

The relevant function for this step of the analysis is call.abnormal.cov function.

For an example of the analysis and the functions you should use, see this script. call.abnormal.cov is called in step 8.

In practice, I would recommend using the automated pipeline and a computing cluster. That way you don't have to deal with all the steps and the jobs are taken care automatically. Don't hesitate if you need assistance.