There are some problem with the documentation where some files are not found. This is caused by the fact that the peaks file format were updated in the Encode project database. If we look into the current encode_df object:
> table(encode_df$experiment$file_format)
bam bed bigBed bigWig CEL csfasta csqual fasta fastq gtf
7058 5092 4915 9639 8 37 38 3 12977 1152
idat tar tsv
126 111 465
We can see that the only format that fit for peaks is bed.
There are some problem with the documentation where some files are not found. This is caused by the fact that the peaks file format were updated in the Encode project database. If we look into the current
encode_dfobject:We can see that the only format that fit for peaks is bed.