convert pfm object to PWM

convert pfm object to PWM

pfm2pwm(x, N = 10000)

Arguments

x	an object of pfm or pcm or matrix
N	Total number of event counts used for pfm generation.

Value

A numeric matrix representing the Position Weight Matrix for PWM.

See also

PWM

Author

Jianhong Ou

Examples

library("MotifDb")
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: ‘BiocGenerics’
#> The following objects are masked from ‘package:parallel’:
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> The following object is masked from ‘package:motifStack’:
#> 
#>     as.data.frame
#> The following objects are masked from ‘package:stats’:
#> 
#>     IQR, mad, sd, var, xtabs
#> The following objects are masked from ‘package:base’:
#> 
#>     anyDuplicated, append, as.data.frame, basename, cbind, colnames,
#>     dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
#>     grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
#>     order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
#>     rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
#>     union, unique, unsplit, which.max, which.min
#> Loading required package: S4Vectors
#> Loading required package: stats4
#> 
#> Attaching package: ‘S4Vectors’
#> The following objects are masked from ‘package:base’:
#> 
#>     expand.grid, I, unname
#> Loading required package: IRanges
#> Loading required package: GenomicRanges
#> Loading required package: GenomeInfoDb
#> Loading required package: Biostrings
#> Loading required package: XVector
#> 
#> Attaching package: ‘Biostrings’
#> The following object is masked from ‘package:grid’:
#> 
#>     pattern
#> The following object is masked from ‘package:base’:
#> 
#>     strsplit
#> See system.file("LICENSE", package="MotifDb") for use restrictions.
matrix.fly <- query(MotifDb, "Dmelanogaster")
pfm2pwm(matrix.fly[[1]])
#>            1          2          3          4            5           6
#> A 0.09058848 0.08109553 0.06942964 0.10678480  0.151543623  0.02239449
#> C 0.08933765 0.07813558 0.08247861 0.03444562 -0.141250984 -0.17397092
#> G 0.07250787 0.07182387 0.04168038 0.11645928 -0.007875448 -0.22545815
#> T 0.11415981 0.12357898 0.13127733 0.08067857 -0.088706937  0.15068829
#>            7          8
#> A 0.09887622 0.10206070
#> C 0.09341600 0.08565662
#> G 0.06059477 0.09743179
#> T 0.11023199 0.09029313