Kindly check the R command

I am doing following in Cooccur library in R.

&开发者_Go百科gt; fb<-read.table("Fb6_peaks.bed")
> f1<-read.table("F16_peaks.bed")

everything is ok with the first two commands and I can also display the data:

> fb
> f1

But when I give the next command as given below

> explore_pairs(c("fb", "f1"))

I get an error message:

Error in sum(sapply(tf1_s, score_sample, tf2_hits = tf2_s, hit_list = hit_l)) : 
  invalid 'type' (list) of argument

Could anyone suggest something?

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Despite promising to release a version to the Bioconductor depository in the article the authors published over a year ago, they have still not delivered. The gz file that is attached to the article is not of a form that my installation recognizes. Your really should be corresponding with the authors for this question.

The nature of the error message suggests that the function is expecting a different data class. You should be looking at the specification for the arguments in the help(explore_pairs) file. If it is expecting 2 matrices, then wrapping data.matrix around the arguments may solve the problem, but if it is expecting a class created by one of that packages functions then you need to take the necessary step to construct the right objects.

The help file for explore_pairs does exist (at least in the MAN directory) and says the first argument should be a character vector with further provisos:

\arguments{
      \item{factornames}{an vector of character strings, each naming a GFF-like
      data frame containing the binding profile of a DNA-binding factor.

There is also a load utility, load_GFF, which I assume is designed for creation of such files.

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Try rename your data frame: names(fb)=c("seq","start","end")

Check the example datasets. The column names are as above. I set the names and it worked.