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deLaatLab / pipe4C

4C-seq processing pipeline
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doPeakC does not exist #6

Closed tamerbio closed 4 years ago

tamerbio commented 4 years ago

Hi everyone, I am using the following command to call peaks: resPeakC <- doPeakC(rdsFiles = rdsFiles)

but it seems that there no such function doPeakC at all!! any idea? best TA

krijgerp commented 4 years ago

Dear TA, The doPeakC function is present in the functions.R file. I just checked the latest version present on Github together with our step-by-step tutorial and it should work. Could you indicate the exact error. Are you using the example data?

tamerbio commented 4 years ago 
> setwd("/test/RDS")
> rdsFiles <- c("s1.rds", "s2.rds")
> resPeakC <- doPeakC(rdsFiles = rdsFiles)
Error in doPeakC(rdsFiles = rdsFiles) : could not find function "doPeakC"
tamerbio commented 4 years ago 
> library(peakC)
> pipe4CFunctionsFile <- "functions.R"
> source(pipe4CFunctionsFile)
Error in file(filename, "r", encoding = encoding) : 
  cannot open the connection
In addition: Warning message:
In file(filename, "r", encoding = encoding) :
  cannot open file 'functions.R': No such file or directory
geertgeeven commented 4 years ago

Dear TA, you need to specify the full path to the pipe4CFunctionsFile. If you navigate for instance to the folder /test/RDS first, with setwd("/test/RDS"), and then type pipe4CFunctionsFile <- "functions.R", this will not work, because functions.R file is not located in /test/RDS/, so you need to write pipe4CFunctionsFile <- "<path to pipe4C>/functions.R", e.g. pipe4CFunctionsFile <- "/home/TA/github/pipe4C/functions.R" if you cloned the pipe4C repository in /home/TA/github/pipe4C/. Hope this helps !

On Thu, Jan 9, 2020 at 1:37 PM tamerbio notifications@github.com wrote:

library(peakC) pipe4CFunctionsFile <- "functions.R" source(pipe4CFunctionsFile) Error in file(filename, "r", encoding = encoding) : cannot open the connection In addition: Warning message: In file(filename, "r", encoding = encoding) : cannot open file 'functions.R': No such file or directory

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