Read a motif file

read_motif_file() reads a motif file and converts to a PWM. The function supports multiple motif formats, including "homer", "jaspar", "meme", "transfac" and "uniprobe".

Usage

read_motif_file(
  motif_file,
  motif_id = "Unknown",
  file_format = "auto",
  verbose = FALSE
)

Arguments

motif_file

Path to a motif file or a universalmotif-class object.

motif_id

ID of the motif (e.g. "MA1930.1").

file_format

Character string specifying the format of the motif file. The options are "homer", "jaspar", "meme", "transfac" and "uniprobe"

verbose

A logical indicating whether to print messages.

Value

A universalmotif motif object.

Examples

motif_file <- system.file("extdata",
                          "motif_MA1930.2.jaspar",
                          package = "MotifPeeker")
res <- read_motif_file(motif_file = motif_file,
                       motif_id = "MA1930.2",
                       file_format = "jaspar")
#> Warning: subscript out of bounds (index 0 >= vector size 0)
print(res)
#> 
#>        Motif name:   MA1930.2
#>    Alternate name:   CTCF
#>          Alphabet:   DNA
#>              Type:   PCM
#>           Strands:   +-
#>          Total IC:   20.69
#>       Pseudocount:   1
#>         Consensus:   CTGCAGTNCNNNNNNNNNNCCASYAGRKGGCRS
#> 
#>      C    T    G    C    A    G    T    N    C    N   N   N    N   N   N   N
#> A  293  242   41   86 1986  445  158  346  453  497 714 536  467 664 563 593
#> C 1497  107   35 2129  127  366  278  324 1333 1129 794 855 1138 604 730 902
#> G  400  144 2476   25  155 1456  179  892  328  419 623 770  561 376 541 494
#> T  386 2083   24  336  308  309 1961 1014  462  531 445 415  410 932 742 587
#>     N    N    N    C    C    A    S    Y    A    G    R    K    G    G    C
#> A 452  560  604  178   38 1906  127  348 2179   32 1140  169   62  119  335
#> C 781  458  300 2074 2515   97 1409 1016   54    9   14   71   14  138 1833
#> G 393 1041 1242  155    9  275  961  175  212 2527 1399 1208 2472 2117   86
#> T 950  517  430  169   14  298   79 1037  131    8   23 1128   28  202  322
#>      R    S
#> A 1021  279
#> C  164 1307
#> G 1161  740
#> T  230  250