Read a HOMER motif file and create a PFMatrixList

Source: R/motif_enrichment_HOMER.R

Read motifs from a file in HOMER format and create a PFMatrixList from them.

homerToPFMatrixList(filename, n = 100L)

Arguments

filename

Name of the input file with HOMER-formatted motifs.

n

The number of observations (multiplied with base frequencies to create the number of observed bases at each position).

Value

A PFMatrixList with motifs from the file.

See also

dumpJaspar for writing motifs from a Jaspar database package into a file in HOMER format.

Examples

library(JASPAR2020)
optsL <- list(ID = c("MA0006.1"))
pfm1 <- TFBSTools::getMatrixSet(JASPAR2020, opts = optsL)
TFBSTools::Matrix(pfm1)
#> $MA0006.1
#>   [,1] [,2] [,3] [,4] [,5] [,6]
#> A    3    0    0    0    0    0
#> C    8    0   23    0    0    0
#> G    2   23    0   23    0   24
#> T   11    1    1    1   24    0
#> 

tmpfn <- tempfile()
dumpJaspar(filename = tmpfn, pkg = "JASPAR2020", opts = optsL)
#> [1] TRUE
pfm2 <- homerToPFMatrixList(tmpfn)
TFBSTools::Matrix(pfm2)
#> [[1]]
#>   [,1] [,2] [,3] [,4] [,5] [,6]
#> A   14    4    4    4    4    4
#> C   32    4   86    4    4    4
#> G   11   86    4   86    4   89
#> T   43    7    7    7   89    4
#> 

unlink(tmpfn)