TFBSTools: Appending objects to PFMatrixList
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@nathanlawlor03-9169
Last seen 4.5 years ago

I have > 2000 motif files (in meme format) which I have imported into R and converted each into PFMatrix objects. Next, I want to store each of these PFMatrix objects into a PFMatrixList object using a "for loop". 

My first thoughts were to store each PFMatrix object into a base list() object as I imported them into R as such:

# move to directory of motif files
fl <- list.files()

# create an empty list
empty.list <- list()
for (i in 1:length(fl)) {
  # load in meme file
  meme <- read.delim(fl[i], ...)
  # create a pfmatrix
  pfm.matrix <- PFMatrix(ID = ...)

  # add PFMatrix object to list
  empty.list <- c(empty.list, pfm.matrix)
}

Instead of a base list() object I would prefer to add these PFMatrix objects to a PFMatrixList object in a similar manner, however, when I try to add a PFMatrix object to an already existing/or empty PFMatrixList object with the PFMatrixList() function, I get the error:

Error in .local(x, use.names, ...) : 
  PFMatrixList() only accepts PFMatrix objects!    
  

 

Is there a way to append PFMatrix objects to an already existing PFMatrixList object?

 

 

 

 

 

TFBSTools looping PFMatrixList PFMatrix bioconductor • 846 views
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Entering edit mode
@nathanlawlor03-9169
Last seen 4.5 years ago

Provided from Ge Tan (author of TFBSTools) a simple solution is:

pfm.list <- do.call(PFMatrixList, empty.list)

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