tidy-motifs: Tidy manipulation of motifs.

In bjmt/universalmotif: Import, Modify, and Export Motifs with R

Tidy manipulation of motifs.

Description

Tidy manipulation of motifs.

Usage

to_df(motifs, extrainfo = TRUE)

update_motifs(motif_df, extrainfo = TRUE, force = FALSE)

to_list(motif_df, extrainfo = TRUE, force = FALSE)

requires_update(motifs, extrainfo = TRUE)

Arguments

motifs	List of motifs.
extrainfo	Use the extrainfo slot in the tidy data.frame. The column names will be taken from the character vectors themselves, and unnamed elements will be assigned a unique name. To add elements to the slot, simply create new columns in the data.frame. Note that these will be coerced into characters. If extrainfo is not set to TRUE in to_df(), then the contents of the slot will not be transferred to the data.frame. If extrainfo is not set to TRUE in update_motifs() or to_list(), then the extra columns will be discarded.
motif_df	Motif data.frame generated by to_df().
force	Whether to coerce non-character data types into characters for inclusion in extrainfo. If force is FALSE (the default), columns which are not of type "character", "numeric", or "integer" (for example, list columns, or logical values), will not be added to the motif extrainfo slot, but will be passed onto the returned universalmotif_df unchanged. Setting force = TRUE coerces these values into a character, adding them to the extrainfo slot, and updating the universalmotif_df columns to reflect this coercion. In other words, forcing inclusion of these data is destructive and will change the column values. Use with caution.

Details

To turn off the informative messages/warnings when printing the object to the console, set options(universalmotif_df.warning=FALSE).

Value

For to_df(): a data.frame with the exposed slots as columns.

For update_motifs(): the updated data.frame.

For requires_update(): TRUE if the motifs are out of date, FALSE if otherwise. Note that this function uses identical() to check for this, which can be quite slow for large datasets. It is usually just as fast to simply run update_motifs() in such cases.

For to_list(): a list of motifs.

Author(s)

Benjamin Jean-Marie Tremblay, [e-mail]

Examples

## Not run: 
library(universalmotif)
library(dplyr)

m <- c(create_motif(name = "motif A"), create_motif(name = "motif B"))

# Change the names of the motifs using the tidy way:
m <- m %>%
   to_df() %>%
   mutate(name = paste0(name, "-2")) %>%
   to_list()

# Add your own metadata to be stored in the extrainfo slot:
m_df <- to_df(m)
m_df$MyMetadata <- c("Info_1", "Info_2")
m <- to_list(m_df, extrainfo = TRUE)

## End(Not run)

bjmt/universalmotif documentation built on March 18, 2024, 8:32 a.m.