Problems with GRanges promoter list for EnrichedHeatmap

Question

[Anwesha_Ghosh]

I am trying to use the package EnrichedHeatmap on Bioconductor. I want to make my own promoters list in GRanges. The demo promoters list for EnrichedHeatmap is of the format:

## GRanges object with 5 ranges and 0 metadata columns:
##                      seqnames               ranges strand
##                         <Rle>            <IRanges>  <Rle>
##    ENSG00000141956.9    chr21 [43299591, 43299591]      -
##   ENSG00000141959.12    chr21 [45719934, 45719934]      +
##    ENSG00000142149.4    chr21 [33245628, 33245628]      +
##   ENSG00000142156.10    chr21 [47401651, 47401651]      +
##    ENSG00000142166.8    chr21 [34696734, 34696734]      +
##   -------
##   seqinfo: 1 sequence from an unspecified genome; no seqlengths

I make my promoters list with:

library(biomaRt)
mart = useMart(biomart = "ENSEMBL_MART_ENSEMBL",
               dataset = "hsapiens_gene_ensembl")
filterlist <- c(1:22, 'X', 'Y')
ds = useDataset('hsapiens_gene_ensembl', mart = mart)
egs = getBM(attributes = c('ensembl_gene_id', 'external_gene_name', 'chromosome_name', 'start_position', 'end_position', 'strand'), 
            filters = 'chromosome_name',
            values = filterlist,
            mart = ds)
egs$TSS = ifelse(egs$strand ==1, egs$start_position, egs$end_position)
head(egs)
promoter_regions = GRanges(egs$ensembl_gene_id,
                           seqnames = Rle(paste0('chr', egs$chromosome_name)),
                           ranges = IRanges(start = egs$TSS - 2000, end = egs$TSS + 2000),
                           strand = Rle(rep("*", nrow(egs))))
head(promoter_regions)

However, my gene id keeps getting added to the last column:

GRanges object with 6 ranges and 1 metadata column:
      seqnames                 ranges strand |            gene
         <Rle>              <IRanges>  <Rle> |     <character>
  [1]     chr1 [111039834, 111043834]      * | ENSG00000252760
  [2]     chr1 [143437605, 143441605]      * | ENSG00000252830
  [3]     chr1 [ 75785889,  75789889]      * | ENSG00000207241
  [4]     chr1 [204725991, 204729991]      * | ENSG00000251861
  [5]     chr1 [211673630, 211677630]      * | ENSG00000117650
  [6]     chr1 [240152772, 240156772]      * | ENSG00000202041
  -------

Hence I get the following error while using

mat_438M <- normalizeToMatrix(BW_438M, promoter, value_column = "coverage", extend = 2000, mean_mode = "w0", w = 50)
Error in tapply(w * v, mtch[, 2], sum, na.rm = TRUE) : 
  arguments must have same length

How can I correct this? Alternatively, what other packages are there that take bigwig files and make heatmaps and profiles? ChIPseeker keeps throwing errors for bigwig files.

Answer 1

[zwdzwd]

You may want to set the names explicitly, since extra positional arguments will be treated as metadata.

promoter_regions = GRanges(seqnames = Rle(paste0('chr', egs$chromosome_name)),
                       ranges = IRanges(start = egs$TSS - 2000, end = egs$TSS + 2000),
                       strand = Rle(rep("*", nrow(egs))))
names(promoter_regions) <- egs$ensembl_gene_id
head(promoter_regions)

outputs

## GRanges object with 6 ranges and 0 metadata columns:
##                   seqnames                 ranges strand
##                     <Rle>              <IRanges>  <Rle>
##  ENSG00000252760     chr1 [111039834, 111043834]      *
##  ENSG00000252830     chr1 [143437605, 143441605]      *
##  ENSG00000207241     chr1 [ 75785889,  75789889]      *
##  ENSG00000251861     chr1 [204725991, 204729991]      *
##  ENSG00000117650     chr1 [211673630, 211677630]      *
##  ENSG00000202041     chr1 [240152772, 240156772]      *
 -------
 seqinfo: 24 sequences from an unspecified genome; no seqlengths