read_matrix {universalmotif} | R Documentation

## Import motifs from raw matrices.

### Description

Import simply formatted motifs.

### Usage

    read_matrix(file, skip = 0, type, positions = "columns",
      alphabet = "DNA", sep = "", headers = TRUE, rownames = FALSE,
      comment = NULL)

### Arguments

`file` | `character(1)` File name.
`skip` | `numeric(1)` If not zero, will skip however many desired lines in the file before starting to read.
`type` | `character(1)` One of `c('PCM', 'PPM', 'PWM', 'ICM')`. If missing will try and guess which one.
`positions` | `character(1)` One of `c('columns', 'rows')`. Partial matching allowed. Indicate whether each position within a motif is represented as a row or a column in the file.
`alphabet` | `character(1)` One of `c('DNA', 'RNA', 'AA')`, or a string of letters.
`sep` | `character(1)` Indicates how individual motifs are separated. Set as `NULL` if there are no seperating lines between motifs (the default is to assume a blank line).
`headers` | `logical(1)`, `character(1)` Indicating if and how to read names.
`rownames` | `logical(1)` Are there alphabet letters present as rownames?
`comment` | `NULL`, `character(1)` Character denoting lines to be considered comments.

### Value

`list` universalmotif objects.

### Author(s)

Benjamin Jean-Marie Tremblay, benjamin.tremblay@uwaterloo.ca

### See Also

Other read_motifs: `read_cisbp()`, `read_homer()`, `read_jaspar()`, `read_meme()`, `read_motifs()`, `read_transfac()`, `read_uniprobe()`

### Examples

       hocomoco <- system.file("extdata", "hocomoco.txt", package = "universalmotif")
       hocomoco <- read_matrix(hocomoco, headers = ">", positions = "rows")

[Package universalmotif version 1.10.2 Index]