Question

Can i set a path for readCodlinkSet()

3

Entering edit mode

Agaz Hussain Wani ▴ 260

@agaz-hussain-wani-7620

Last seen 6.6 years ago

India

Hello everybody,

I am trying to read some files from temporary path to do differential expression using codlink package. I have phenotype files on the same path which i read by

pdata = read.AnnotatedDataFrame(lst[i],path=newpath,sep="")

and it works happily

Now when i call

codset = readCodelinkSet(filename = pdata$FileName,phenoData = pdata)

It gives an error saying cannot open connection, which is quite obvious as my files are not in the local directory but on the temporary path. So is there an option to set the path which currently i don't find in readCodelinkSet(). I mean something like

codset = readCodelinkSet(filename = pdata$FileName,path=...,phenoData = pdata)

Or is there an alternate option to do it.

r differential expression codelink • 2.1k views

ADD COMMENT • link updated 9.4 years ago by Diego Diez ▴ 760 • written 9.5 years ago by Agaz Hussain Wani ▴ 260

score 1 · Accepted Answer · 2015-06-17

1

Entering edit mode

Diego Diez ▴ 760

@diego-diez-4520

Last seen 4.1 years ago

Japan

Hi hussainaaghaz,

You are right that there is no way to specify the path in readCodelinkSet. I may change this in the future. In the meantime you can use the following workaround:

# append path to file names:
newpath <- "my/new/path"
pdata$FileNames <- file.path(newpath, pdata$FileNames)

# then, this should work:
codset <- readCodelinkSet(filename = pdata$FileNames)

ADD COMMENT • link 9.4 years ago Diego Diez ▴ 760

0

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Hi dear Diego,

I tried your code but got an error:

## this line gives an error

pdata$FileNames <- file.path(newpath, pdata$FileNames)

Error in `[[<-.data.frame`(`*tmp*`, i, value = character(0)) : replacement has 0 rows, data has 4

My pdata looks like

  FileName       Treatment  Condition
1 GSM108293.TXT   C         1
2 GSM108294.TXT   C         1
3 GSM108295.TXT   Tu        2
4 GSM108290.TXT   Tu        2

ADD REPLY • link 9.4 years ago Agaz Hussain Wani ▴ 260

1

Entering edit mode

In my example the column with the file names is called "FileNames" in your data is called "FileName" hence the error. Try fixing the column name: pdata$FileName <- file.path(newpath, pdata$FileName)

ADD REPLY • link 9.4 years ago Diego Diez ▴ 760

0

Entering edit mode

Oh... !! Yes you are absolutely right . Thanks

ADD REPLY • link 9.4 years ago Agaz Hussain Wani ▴ 260

score 1 · Accepted Answer · 2015-06-24

1

Entering edit mode

Diego Diez ▴ 760

@diego-diez-4520

Last seen 4.1 years ago

Japan

FYI, I have added this feature to the development version of Bioconductor, and should be generally available for the next release: https://github.com/ddiez/codelink/issues/1

Basically, readCodelinkSet() now accepts a path argument. For example:

codset <- readCodelinkSet(filename = "myfiles", path = "my/new/path")