import motifs from local files

Import the motifs into pcm-class or pfm-class from files exported from Transfac, CisBP, and JASPAR.

importMatrix(
  filenames,
  format = c("auto", "pfm", "cm", "pcm", "meme", "transfac", "jaspar", "scpd", "cisbp",
    "psam"),
  to = c("auto", "pcm", "pfm", "pssm", "psam")
)

Arguments

filenames	filename to be imported.
format	file format
to	import to pcm-class or pfm-class

Value

a list of object pcm-class or pfm-class

Author

Jianhong Ou

Examples

  path <- system.file("extdata", package = "motifStack")
  importMatrix(dir(path, "*.pcm", full.names = TRUE))
#> $bin_SOLEXA
#> An object of class "pcm"
#> Slot "mat":
#>   [,1] [,2] [,3] [,4] [,5] [,6] [,7]
#> A  462    0 1068 1025 1068    0 1019
#> C   71   60    0   24    0  993    0
#> G  504    0    0    0    0   12    0
#> T   31 1008    0   19    0   63   49
#> 
#> Slot "name":
#> [1] "bin_SOLEXA"
#> 
#> Slot "alphabet":
#> [1] "DNA"
#> 
#> Slot "color":
#>         A         C         G         T 
#> "#00811B" "#2000C7" "#FFB32C" "#D00001" 
#> 
#> Slot "background":
#>    A    C    G    T 
#> 0.25 0.25 0.25 0.25 
#> 
#> Slot "tags":
#> list()
#> 
#> Slot "markers":
#> list()
#> 
#> 
#> $fd64A_SOLEXA
#> An object of class "pcm"
#> Slot "mat":
#>   [,1] [,2] [,3] [,4] [,5] [,6] [,7]
#> A    0   47    0    0    0  347   15
#> C    0    0    0    0    0    0  208
#> G    0  504    0    5   61   98  112
#> T  551    0  551  546  490  106  216
#> 
#> Slot "name":
#> [1] "fd64A_SOLEXA"
#> 
#> Slot "alphabet":
#> [1] "DNA"
#> 
#> Slot "color":
#>         A         C         G         T 
#> "#00811B" "#2000C7" "#FFB32C" "#D00001" 
#> 
#> Slot "background":
#>    A    C    G    T 
#> 0.25 0.25 0.25 0.25 
#> 
#> Slot "tags":
#> list()
#> 
#> Slot "markers":
#> list()
#> 
#> 
#> $fkh_NAR
#> An object of class "pcm"
#> Slot "mat":
#>   [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11]
#> A    3    5    0    0    0   13    4    6    0    23    15
#> C    0    0    0    0    0    0   13    7   11     0     4
#> G    0   22    0    0    1   14    2    3    2     1     4
#> T   24    0   27   27   26    0    8   11   14     3     4
#> 
#> Slot "name":
#> [1] "fkh_NAR"
#> 
#> Slot "alphabet":
#> [1] "DNA"
#> 
#> Slot "color":
#>         A         C         G         T 
#> "#00811B" "#2000C7" "#FFB32C" "#D00001" 
#> 
#> Slot "background":
#>    A    C    G    T 
#> 0.25 0.25 0.25 0.25 
#> 
#> Slot "tags":
#> list()
#> 
#> Slot "markers":
#> list()
#> 
#> 
#> $foxo_SOLEXA
#> An object of class "pcm"
#> Slot "mat":
#>   [,1] [,2] [,3] [,4] [,5] [,6] [,7]
#> A    0  122    0    0  107  978    8
#> C    0   16    0    0    0    0  834
#> G    0 1443    2    5   96  163  191
#> T 1581    0 1579 1576 1378  440  516
#> 
#> Slot "name":
#> [1] "foxo_SOLEXA"
#> 
#> Slot "alphabet":
#> [1] "DNA"
#> 
#> Slot "color":
#>         A         C         G         T 
#> "#00811B" "#2000C7" "#FFB32C" "#D00001" 
#> 
#> Slot "background":
#>    A    C    G    T 
#> 0.25 0.25 0.25 0.25 
#> 
#> Slot "tags":
#> list()
#> 
#> Slot "markers":
#> list()
#> 
#> 
#> $FoxP_SOLEXA
#> An object of class "pcm"
#> Slot "mat":
#>   [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
#> A  380   52 1158 1178 1202    0 1191  651
#> C   83  184   44   24    0 1057    0  151
#> G  652    1    0    0    0    0    1  154
#> T    5  958    0    0    0  145    0  209
#> 
#> Slot "name":
#> [1] "FoxP_SOLEXA"
#> 
#> Slot "alphabet":
#> [1] "DNA"
#> 
#> Slot "color":
#>         A         C         G         T 
#> "#00811B" "#2000C7" "#FFB32C" "#D00001" 
#> 
#> Slot "background":
#>    A    C    G    T 
#> 0.25 0.25 0.25 0.25 
#> 
#> Slot "tags":
#> list()
#> 
#> Slot "markers":
#> list()
#> 
#> 
#> $slp1_SOLEXA
#> An object of class "pcm"
#> Slot "mat":
#>   [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9]
#> A  844  290  641  351 1747 1832 1851    0 1842
#> C  361  642  432  302  104   19    0 1710    9
#> G  482  277  745    7    0    0    0   14    0
#> T  158  642   33 1191    0    0    0  127    0
#> 
#> Slot "name":
#> [1] "slp1_SOLEXA"
#> 
#> Slot "alphabet":
#> [1] "DNA"
#> 
#> Slot "color":
#>         A         C         G         T 
#> "#00811B" "#2000C7" "#FFB32C" "#D00001" 
#> 
#> Slot "background":
#>    A    C    G    T 
#> 0.25 0.25 0.25 0.25 
#> 
#> Slot "tags":
#> list()
#> 
#> Slot "markers":
#> list()
#> 
#> 
#> $slp2_SOLEXA
#> An object of class "pcm"
#> Slot "mat":
#>   [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
#> A  257    0  101    0    0    0  938   31
#> C  168    0    0    0    0    0    0  613
#> G  194    0 1143    0   18   58  111  152
#> T  590 1244    0 1244 1226 1186  195  448
#> 
#> Slot "name":
#> [1] "slp2_SOLEXA"
#> 
#> Slot "alphabet":
#> [1] "DNA"
#> 
#> Slot "color":
#>         A         C         G         T 
#> "#00811B" "#2000C7" "#FFB32C" "#D00001" 
#> 
#> Slot "background":
#>    A    C    G    T 
#> 0.25 0.25 0.25 0.25 
#> 
#> Slot "tags":
#> list()
#> 
#> Slot "markers":
#> list()
#> 
#>