readMotifs: Read in motifs in JASPAR or TRANSFAC format

Description Usage Arguments Value Examples

View source: R/readData.R

Description

The format is autodetected based on file format. If the autodetection fail then the file cannot be read.

Usage

1
  readMotifs(file, remove.acc = FALSE)

Arguments

file

the filename

remove.acc

if to remove accession numbers. If TRUE, the AC entry in TRANSFAC files is ignored, and the accession is stripped from JASPAR, e.g. motif with name "MA0211.1 bap" would become just "bap". If FALSE, botht he AC and ID are used to generate the TRANSFAC name and the original motif names are preserved in JASPAR files.

Value

a list of 4xL matrices representing motifs (four nucleotides as rows)

Examples

1
2
3
4
5
# read in example TRANSFAC motifs without accession codes (just IDs)
readMotifs(system.file(package="PWMEnrich", dir="extdata", file="example.transfac"), remove.acc=TRUE)

# read in the JASPAR insects motifs provided as example
readMotifs(system.file(package="PWMEnrich", dir="extdata", file="jaspar-insecta.jaspar"), remove.acc=TRUE)

Example output

Loading required package: grid
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 objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

$tin_like_motif
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
A   12    5    2    1    0   36   37    0    0     0     5     4     8    10
C   10    7   24    0   36    0    0    1    0     0     6    19     8     4
G   10   13    6    0    0    1    0   36    0    36    22     7     6     8
T    5   12    5   36    1    0    0    0   37     1     4     7    15    15

$gata_like_motif
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11]
A   17   17   13   42    0   42    0   42    0    21    12
C    7   12   19    0    0    0    0    0   42     5    16
G    6    6    7    0   42    0    0    0    0     8     5
T   12    7    3    0    0    0   42    0    0     8     9

$br_Z1
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
A    3    1    5    7    3    6    4    7    1     9     8     5     4     2
C    1    1    2    0    0    0    1    0    8     0     0     0     0     3
G    4    1    1    1    0    0    4    1    0     0     1     3     0     2
T    1    6    1    1    6    3    0    1    0     0     0     1     5     2

$br_Z2
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
A    3    5    0    0   12    1    2    1
C    1    2   10    1    0    1    0    2
G    1    1    0    0    0    2    1    1
T    7    4    2   11    0    8    9    8

$br_Z3
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11]
A    3    9   10   12    0    4   10    6    6     4     2
C    1    2    0    0   10    0    0    0    1     3     3
G    1    1    0    0    1    0    0    4    2     2     5
T    7    0    2    0    1    8    2    2    3     3     2

$br_Z4
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11]
A    1    4    2    1    5    6    5    1    3     5     3
C    1    0    0    0    0    0    0    3    0     0     1
G    0    0    4    0    1    0    1    1    1     0     0
T    4    2    0    5    0    0    0    1    2     1     2

$Cf2_II
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
A   25    1   74    0   78    1   41    2   53    12
C   13    2    2    9    2    4    2    9    3    29
G   40    1    4    4    0    1   36    1   20    15
T    2   76    0   67    0   74    1   68    4    24

$usp
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
A    0    1    0    0    0    0   35    5    5     6
C    1    0    0    0    0   36    0   25    8    10
G   37   36   38   38    0    1    3    3   22    16
T    0    1    0    0   38    1    0    5    3     6

$dl_1
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
A    0    0    0    0    1    1    1    0    0     1     1     3
C    5    0    1    0    1    0    0    0    3     9     9     5
G    6   12   11   10    3    2    0    0    0     0     1     5
T    2    1    1    3    8   10   12   13   10     3     2     0

$dl_2
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
A    0    0    0    0    4    2    0    0    0     1
C    1    0    0    0    1    1    0    1    9     8
G    7    7    9    8    0    0    0    0    0     0
T    1    2    0    1    4    6    9    8    0     0

$Eip74EF
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    2    5    0    0   17   17    5
C   12   12    0    0    0    0    1
G    2    0   17   17    0    0   10
T    1    0    0    0    0    0    1

$hb
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
A    1    6    9    4   13   16   16   14   15     9
C    5    8    3    3    1    0    0    0    1     2
G    8    2    4    1    0    0    0    2    0     2
T    2    0    0    8    2    0    0    0    0     3

$`Su(H)`
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
A    1    0    0    0    0    3    0   10   10     5     1     1     4     3
C    3    4    0    0    0    0    0    0    0     5     7     2     2     1
G    3    0   10    0   10    7   10    0    0     0     1     4     2     4
T    3    6    0   10    0    0    0    0    0     0     1     3     2     2
  [,15] [,16]
A     4     2
C     3     1
G     2     2
T     1     5

$sna
  [,1] [,2] [,3] [,4] [,5] [,6]
A    0   39    3    2    0    0
C   39    0    0    0    0    0
G    1    0   37   38    0   38
T    0    1    0    0   40    2

$Ubx
  [,1] [,2] [,3] [,4]
A    3   72   79    1
C    0    4    1    5
G    0    3    6    4
T   85    9    2   78

$ovo
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9]
A   10    1    4   20   21    0    7    0    5
C    4    4    2    0    0   21    5    0    4
G    0   14    2    0    0    0    3   21    2
T    7    2   13    1    0    0    6    0   10

$`Abd-B`
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    1    0    5   21    0    3   13
C    0    0    0    0    3    0    0
G    0    0    0    0    0   11    5
T   20   21   16    0   18    7    3

$Antp
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    1    0   16   16    0    0   15
C    1    0    0    0    0    0    0
G    0    0    0    0    0    9    1
T   14   16    0    0   16    7    0

$Awh
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    3    1   33   40    0    0   34
C   16    0    0    0    0    0    0
G    0    0    7    0    1    8    4
T   21   39    0    0   39   32    2

$`B-H1`
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    4    0   21   21    8    1    1
C    4    0    0    0    0    7    0
G    0    0    0    0    0    0   20
T   13   21    0    0   13   13    0

$`B-H2`
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    6    0   21   21    5    3    0
C    2    0    0    0    0    1    0
G    1    0    0    0    0    2   21
T   12   21    0    0   16   15    0

$C15
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    1    0   17   19    6    0   10
C    1    0    0    0    2    3    0
G    0    0    0    0    0    6    9
T   17   19    2    0   11   10    0

$CG11085
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    0    0   13   13    1    2    1
C    3    0    0    0    0    1    0
G    0    0    0    0    0    2   12
T   10   13    0    0   12    8    0

$CG11294
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    0    0   15   15    0    0   15
C    3    2    0    0    0    0    0
G    0    0    0    0    0    0    0
T   12   13    0    0   15   15    0

$CG11617
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    1    0   10   17    0   17    0
C    0    0    0    0   17    0    0
G    0    0    3    0    0    0    0
T   16   17    4    0    0    0    1

$CG42234
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    2    2    6   16    0    0   13
C    0    0    0    0    0    2    0
G    0    0    2    0    0    6    3
T   14   14    8    0   16    8    0

$CG13424
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    2    0   21   21    0    3    8
C    7    0    0    0    0    0    0
G    1    0    0    0    0    4   13
T   11   21    0    0   21   14    0

$CG15696
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    2    2   21   32    0    0   16
C    3    3    0    0    0    0    0
G    3    0    6    0    0    2   16
T   24   27    5    0   32   30    0

$CG18599
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    4    0   25   25    0    0   23
C   10    0    0    0    0    1    0
G    1    0    0    0    0    8    2
T   10   25    0    0   25   16    0

$CG32105
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    2    2   17   19    0    0   15
C    4    0    0    0    0    0    0
G    0    0    0    0    1    1    4
T   13   17    2    0   18   18    0

$CG32532
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    2    0   23   23    0    0   12
C    6    0    0    0    0    0    0
G    2    0    0    0    0    2   10
T   13   23    0    0   23   21    1

$Vsx2
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9]
A    1    2    0   13   13    0    0   10    1
C    1    2    0    0    0    0    0    0    2
G    5    0    0    0    0    0    0    3   10
T    6    9   13    0    0   13   13    0    0

$Vsx1
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    1    0   22   22    0    2   15
C    8    0    0    0    0    0    0
G    1    0    0    0    0    3    6
T   12   22    0    0   22   17    1

$CG4328
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A   12    7   13   30    0    0   15
C    2    1    0    0    0    0    0
G    3    0    0    0    0    6   15
T   13   22   17    0   30   24    0

$CG7056
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
A    7    0    0   21   26    0    7   22
C    3    7    6    0    0    3    0    0
G    2    0    7    2    0    3    1    4
T   14   19   13    3    0   20   18    0

$CG9876
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    2    0   18   20    0    0   14
C    9    0    0    0    0    0    0
G    3    0    0    0    0    1    6
T    6   20    2    0   20   19    0

$Deaf1
  [,1] [,2] [,3] [,4] [,5] [,6]
A    0    0    0    0    0    1
C    3    0   10    0    0    3
G    0    0    0   10    5    4
T    7   10    0    0    5    2

$Dfd
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    1    0   24   24    0    1   21
C    4    0    0    0    0    0    0
G    3    0    0    0    0   19    3
T   16   24    0    0   24    4    0

$Dll
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    1   22   23    0    3   10    1
C    0    0    0    0    0    0   12
G    0    1    0    0    3    9    4
T   22    0    0   23   17    4    6

$Dr
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    1    0   21   21    0    0   21
C   13   16    0    0    0    0    0
G    6    0    0    0    0    0    0
T    1    5    0    0   21   21    0

$E5
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    5    3   43   42    1    5   34
C   15    0    0    0    0    0    0
G    6    0    0    0    1   16    9
T   17   40    0    1   41   22    0

$Gsc
  [,1] [,2] [,3] [,4] [,5] [,6]
A    0   22   22    0    0    0
C    0    0    0    0   22   14
G    0    0    0    0    0    2
T   22    0    0   22    0    6

$HGTX
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    4    0   20   20    0    1   15
C    2    0    0    0    0    0    0
G    3    0    0    0    0    6    5
T   11   20    0    0   20   13    0

$Hmx
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    1    0   20   20    1    0    4
C    3    0    0    0    0    3    0
G    0    0    0    0    0    0   16
T   16   20    0    0   19   17    0

$Lag1
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    0    0   17    1    0   18   12
C   19    9    2   18   12    0    0
G    0    0    0    0    0    1    4
T    0   10    0    0    7    0    3

$Lim1
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    0    0   18   18    0    0   17
C    2    0    0    0    0    0    0
G    0    0    0    0    0    0    1
T   16   18    0    0   18   18    0

$Lim3
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    3    4   16   20    0    0   16
C    7    0    0    0    0    2    0
G    2    0    3    0    0    4    4
T    8   16    1    0   20   14    0

$NK7.1
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    5    0   33   35    4    6   13
C    5    0    0    0    0    0    0
G    1    0    2    0    5    7   22
T   24   35    0    0   26   22    0

$Oct
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
A    2    8    1   22   22    0    2   15
C    4    3    0    0    0    0    3    1
G    7    0    0    0    0    0    6    1
T    9   11   21    0    0   22   11    5

$OdsH
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    0    0   22   22    0    0   13
C   11    0    0    0    0    0    0
G    4    0    0    0    0    0    8
T    7   22    0    0   22   22    1

$Optix
  [,1] [,2] [,3] [,4] [,5]
A    0    0   27    0   26
C    5    0    0    0    0
G    0   27    0    0    1
T   22    0    0   27    0

$Pph13
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    6    0   21   21    0    0   13
C    8    0    0    0    0    1    1
G    3    0    0    0    0    0    6
T    4   21    0    0   21   20    1

$Ptx1
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    0    0   20   20    0    0    0
C    5    0    0    0    0   20   19
G    1    0    0    0    0    0    0
T   14   20    0    0   20    0    1

$Rx
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    3    0   27   27    0    0   17
C   13    0    0    0    0    0    0
G    0    0    0    0    0    0   10
T   11   27    0    0   27   27    0

$Scr
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    3    0   25   25    0    0   23
C    7    0    0    0    0    0    0
G    0    0    0    0    0   18    2
T   15   25    0    0   25    7    0

$Six4
  [,1] [,2] [,3] [,4] [,5] [,6]
A    0    0   20    0   20    1
C    0    0    0    7    0   19
G    0   20    0    4    0    0
T   20    0    0    9    0    0

$Trl
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
A    4    6   12    0    3    1   13    5    7     9
C   22   23    6   64    0   70    0   54   13    33
G    9   11   30    3   14    0    2    7   11    10
T   36   31   23    4   54    0   56    5   40    19

$`abd-A`
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    1    0   16   18    1    0   15
C    3    0    0    0    0    0    1
G    0    0    0    0    0    6    2
T   14   18    2    0   17   12    0

$achi
  [,1] [,2] [,3] [,4] [,5] [,6]
A    0    0   23    0   23    3
C    0    0    0   22    0    0
G    0   23    0    0    0   12
T   23    0    0    1    0    2

$al
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    0   20   20    0    0   17   18
C    0    0    0    0    0    0    0
G    0    0    0    0    0    3    2
T   20    0    0   20   20    0    0

$ap
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    2    1   19   19    0    0   16
C   10    0    0    0    0    0    0
G    0    0    0    0    0    6    3
T    7   18    0    0   19   13    0

$ara
  [,1] [,2] [,3] [,4] [,5]
A   14   23   34    0   34
C    0    0    0   34    0
G    5    0    0    0    0
T   15   11    0    0    0

$bap
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    0    0   23   23    0    1    7
C    0    0    0    0    0    0    0
G    1    0    0    0   23    0   16
T   22   23    0    0    0   22    0

$bcd
  [,1] [,2] [,3] [,4] [,5] [,6]
A    0   20   22    0    0    0
C    0    0    0    0   22   21
G    0    0    0    1    0    0
T   22    2    0   21    0    1

$brk
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
A    1    0    0    0    0    1    1    0
C    5    4    0    0   10    0    8    5
G    4    0   10   10    0    9    0    1
T    0    6    0    0    0    0    1    4

$bsh
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    1    0   16   16    0    0    7
C    3    0    0    0    1    3    0
G    2    0    0    0    0    6    9
T   10   16    0    0   15    7    0

$btn
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    5    0   22   23    0    0   19
C    1    0    0    0    1    0    0
G    4    0    1    0    0   15    3
T   13   23    0    0   22    8    1

$cad
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    3    1    8   37    3    3   18
C    2    0    0    0    0    0    0
G    3    0    2    1    0    9   19
T   30   37   28    0   35   26    1

$caup
  [,1] [,2] [,3] [,4] [,5]
A    4   14   19    0   19
C    1    0    0   19    0
G    2    2    0    0    0
T   12    3    0    0    0

$ct
  [,1] [,2] [,3] [,4] [,5] [,6]
A    0    1    9   20   17    0
C    6    2    0    0    0   19
G    0    0   11    0    1    1
T   14   17    0    0    2    0

$ems
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    3    3   19   19    0    0   14
C    7    0    0    0    0    1    0
G    1    0    0    1    0   10    6
T    9   17    1    0   20    9    0

$en
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    2    0   23   23    0    0   13
C    8    0    0    0    0    0    0
G    2    0    0    0    0    2   10
T   11   23    0    0   23   21    0

$eve
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    3    1   22   22    0    0   17
C   10    0    0    0    2    2    0
G    0    0    0    0    1   11    4
T    9   21    0    0   19    9    1

$exd
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
A    4    1    0    0    0   17    0   11
C    4    0    0    0    0    0   12    0
G    4    2    0    0   17    0    0    6
T    5   14   17   17    0    0    5    0

$exex
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    0    0   23   23    0    1   20
C    7    0    0    0    0    1    0
G   10    0    0    0    0    0    3
T    6   23    0    0   23   21    0

$exex
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    0    0   23   23    0    1   20
C    7    0    0    0    0    1    0
G   10    0    0    0    0    0    3
T    6   23    0    0   23   21    0

$ftz
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    1    1   18   18    0    0   14
C    2    0    0    0    0    0    0
G    0    0    0    0    0    9    4
T   15   17    0    0   18    9    0

$hbn
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    2    0   17   17    0    0    9
C    2    0    0    0    0    0    0
G    2    0    0    0    0    0    7
T   11   17    0    0   17   17    1

$hth
  [,1] [,2] [,3] [,4] [,5] [,6]
A    0    0   17    0   14    0
C    0    0    0   17    0    0
G    0   17    0    0    3    8
T   17    0    0    0    0    4

$ind
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    0    0   21   21    0    0   19
C   12    0    0    0    0    0    0
G    0    0    0    0    1    8    2
T    9   21    0    0   20   13    0

$inv
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
A    4    1    0   16   16    0    0   11
C    0    9    0    0    0    0    0    0
G    3    0    0    0    0    0    0    5
T    9    6   16    0    0   16   16    0

$lab
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    1    0   16   16    1    0   16
C    3    0    0    0    0    0    0
G    0    0    0    0    0    6    0
T   12   16    0    0   15   10    0

$lbe
  [,1] [,2] [,3] [,4] [,5] [,6]
A    0   22   22    1    4   19
C    0    0    0   10    5    0
G    0    0    0    2    3    3
T   22    0    0    9   10    0

$lbl
  [,1] [,2] [,3] [,4] [,5] [,6]
A    0   23   23    0    1   17
C    0    0    0    5    3    0
G    0    0    0    0    7    6
T   23    0    0   18   12    0

$mirr
  [,1] [,2] [,3] [,4] [,5]
A   20   29   41    0   41
C    1    0    0   41    0
G    1    2    0    0    0
T   19   10    0    0    0

$oc
  [,1] [,2] [,3] [,4] [,5] [,6]
A    0   19   19    0    0    0
C    0    0    0    0   19   17
G    0    0    0    2    0    1
T   19    0    0   17    0    1

$onecut
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    1    0    0   15    0    0    5
C    2    0    0    0    0    0    0
G    0    0   15    0    0    0    4
T   12   15    0    0   15   15    6

$otp
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    1    0   20   20    0    0   15
C    6    1    0    0    0    1    0
G    2    0    0    0    0    4    3
T   11   19    0    0   20   15    2

$pan
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
A    4    2    2    2    0   17    8    7
C   10    3    0    0    2    0    0   11
G    3    0    1    0   20    5    0    3
T    8   20   22   23    3    3   17    4

$pb
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    4    0   24   24    0    0   24
C    9    0    0    0    0    0    0
G    0    0    0    0    0   11    0
T   11   24    0    0   24   13    0

$prd
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9]
A   10    1    4   20   21    0    7    0    5
C    4    4    2    0    0   21    5    0    4
G    0   14    2    0    0    0    3   21    2
T    7    2   13    1    0    0    6    0   10

$repo
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    1    1   27   28    0    0   21
C    4    0    0    0    0    0    0
G    4    0    0    0    0    0    7
T   19   27    1    0   28   28    0

$ro
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    1    0   23   23    0    0   19
C   12    0    0    0    0    0    0
G    3    0    0    0    0    3    4
T    7   23    0    0   23   20    0

$`run::Bgb`
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9]
A   12   27   28    0    0    5    0   28   20
C    2    0    0   29   28    1   29    0    0
G    0    1    1    0    1   23    0    0    9
T   15    1    0    0    0    0    0    1    0

$sd
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
A    3    8    4   14    1    3    0    3    4     5     5     4
C    0    1    8    0    1    0    8    5    1     6     1     3
G    8    1    1    0    0    1    0    3    2     3     7     4
T    3    4    1    0   12   10    6    3    7     0     1     3

$slbo
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
A    9    0    0    3    2    7    6   11
C    1    1    0    2   10    2    5    1
G    1    0    3    7    0    2    1    0
T    1   11    9    0    0    1    0    0

$slou
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    3    0   22   21    0    2   11
C    5    1    0    0    0    1    0
G    1    0    0    1    0    5   11
T   13   21    0    0   22   14    0

$so
  [,1] [,2] [,3] [,4] [,5] [,6]
A    0    0   27    0   27    0
C    0    0    0    0    0   10
G    1   27    0    1    0    0
T   26    0    0   26    0    3

$tin
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
A    0    1    0   16   16    0    0    3
C    9    0   11    0    0    0    0    0
G    3    0    1    0    0   16    0   13
T    4   15    4    0    0    0   16    0

$tup
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    4    1   16   16    0    1    2
C    2    0    0    0    0    0    0
G    1    0    0    0    2    7   13
T    9   15    0    0   14    8    1

$twi
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
A    1    3    1    0   11    0    7    0    0     1     1     2
C    4    7    3   14    3    4    1    0    0     0     2     3
G    3    3   10    1    1    1    5    0   12     2     2     8
T    7    2    1    0    0   10    2   15    3    12    10     2

$`unc-4`
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    1    0   21   21    0    1    6
C    5    0    0    0    0    0    1
G    2    0    0    0    0    0   14
T   13   21    0    0   21   20    0

$unpg
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    1    1   21   21    0    0   14
C    6    0    0    0    0    0    0
G    4    0    0    0    0    2    7
T   10   20    0    0   21   19    0

$vis
  [,1] [,2] [,3] [,4] [,5] [,6]
A    0    0   22    0   22    2
C    0    0    0   22    0    4
G    0   22    0    0    0    8
T   22    0    0    0    0    2

$vnd
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9]
A    4    1    0    0   19   19    0    2    9
C    0    8    0   15    0    0    0    0    0
G    2    1    0    2    0    0   19    0   10
T   13    9   19    2    0    0    0   17    0

$vvl
  [,1] [,2] [,3] [,4] [,5] [,6]
A    0   11    2    0    3   11
C    2    0    2    0    8    0
G    0    0    0    6    0    0
T    9    0    7    5    0    0

$z
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
A   11    1    1   41    1    8    2   18   10    14
C    3    7    0    0    0   10    6    7    5     6
G    5    3   40    0   40    0   29   11   12     2
T   22   30    0    0    0   23    4    5   14    19

$zen
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    2    0   16   16    0    0   16
C    9    0    0    0    0    0    0
G    0    0    0    0    0   11    0
T    5   16    0    0   16    5    0

$zen2
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    3    1   26   26    0    0   22
C    7    0    0    0    1    0    0
G    5    0    0    0    0   10    4
T   11   25    0    0   25   16    0

$Ubx
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
A    3    0    0   17   20    0    0   14
C    5    0    0    0    0    0    0    0
G    3    0    0    0    0    0    6    6
T    9   20   20    3    0   20   14    0

$btd
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
A   14   10    4    2    0    0    2    0    0    15
C    3    0    0    0    0    0   28    0    0     1
G    7   20   18   28   30   30    0   30   20    10
T    6    0    8    0    0    0    0    0   10     4

$CG34031
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    0    0   22   25    2    7    3
C    1    0    0    0    0    0    0
G    1    0    0    0    0    1   22
T   23   25    3    0   23   17    0

$D
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11]
A    1    0    0   20    0    0    2    0    1     4     6
C    8   25   17    0    0    0    0    0    2    10     1
G    7    0    0    0    0    3   27    0    4     6     1
T   13    4   12    9   29   26    0   29   22     9    21

$fkh
  [,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

$gt
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
A   28    0    1   54    0    7    0   55   60     2
C    5    0    1    0   53    0    6    3    0    25
G   25    0    3    6    0   53    0    1    0     5
T    2   60   55    0    7    0   54    1    0    28

$H2.0
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    6    2   16   31    0    8   24
C    3    1    1    0    0    0    0
G    4    0    1    0    0    9    7
T   19   29   14    1   32   15    1

$h
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
A    1    3    1   22    1    2    1    1    7     1
C    2    7   31    1   30    1   10    1   17    30
G   30   17    1   10    1   30    1   31    7     2
T    1    7    1    1    2    1   22    1    3     1

$hkb
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9]
A    3    8    0    0    0    0    0    0   24
C    0    0    0    0   32    0    0    0    3
G   18   24   32   32    0   32    3   31    2
T   11    0    0    0    0    0   29    1    3

$kni
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
A   19   25   16    5    0   21    0   17    1     0    25     5
C    1    1    0    9    4    0    0    0    3    26     0    12
G    2    0    0    6    1    5   26    8   18     0     1     7
T    4    0   10    6   21    0    0    1    4     0     0     2

$Kr
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11]
A    3   11   24   30   18    0    2    2    0     4    20
C   17    4    0    0    6    0    0    0    1     0     4
G    5   10    7    0    7   31   29   29    7     5     3
T    6    6    0    1    0    0    0    0   23    22     4

$nub
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
A    2   29    0    0    0   24   28   28    4     6    19     4
C    1    0    0    0   19    0    0    0    1     5     5     3
G    1    0    0   25    1    0    1    0    0     8     1    15
T   25    0   29    4    9    5    0    1   24    10     4     7

$odd
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11]
A    7   10    0   12    0    0   15    0    0    11     5
C    5    5   14    0    0    0    0    0   15     3     4
G    0    0    1    3   15    0    0   15    0     1     6
T    3    0    0    0    0   15    0    0    0     0     0

$OdsH
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    0    0   22   22    0    0   13
C   11    0    0    0    0    0    0
G    4    0    0    0    0    0    8
T    7   22    0    0   22   22    1

$opa
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
A    0   10    1    1    0    0    0    0    4     0     3     2
C    1    7   16   15   16   18   18   14    0    14     1     0
G   15    1    0    1    1    0    0    0   13     2     4    16
T    2    0    1    1    1    0    0    4    1     2    10     0

$PHDP
  [,1] [,2] [,3] [,4] [,5] [,6] [,7]
A    4    0   16   17    0    1    8
C    6    0    0    0    0    0    1
G    0    0    0    0    0    1    4
T    7   17    1    0   17   15    4

$slp1
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11]
A    8    0    3    0    0    0   27    1   17     4    15
C    3    0    0    0    0    0    0   22    8    13     3
G   14    0   38    0    1    2    4    7   15     3     4
T   16   41    0   41   40   39   10   11    1    21    19

$tll
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
A   20   29   33   31    0    0    0   33   31    17
C    4    0    0    1    0    2   33    0    0    10
G    4    4    0    1   33    0    0    0    1     2
T    5    0    0    0    0   31    0    0    1     4

$ttk
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9]
A   10   22    0    0   22    0   21   22    1
C    8    0    0    0    0    5    0    0    5
G    3    0   22   22    0    0    0    0    3
T    1    0    0    0    0   17    1    0   13

PWMEnrich documentation built on Nov. 1, 2018, 2:25 a.m.