read_matrix: Import motifs from raw matrices.
In universalmotif: Import, Modify, and Export Motifs with R

Import simply formatted motifs.

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

`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.
`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.

list universalmotif objects.

Benjamin Jean-Marie Tremblay, b2tremblay@uwaterloo.ca

1 2	hocomoco <- system.file("extdata", "hocomoco.txt", package = "universalmotif") hocomoco <- read_matrix(hocomoco, headers = ">", positions = "rows")