importTomTomXML: Import tomtom data from previous run

In snystrom/dremeR: motif matching, comparison, and de novo discovery using the MEME Suite

Import tomtom data from previous run

Description

Import tomtom data from previous run

Usage

importTomTomXML(tomtom_xml_path)

Arguments

tomtom_xml_path

path to tomtom.xml

Details

tomtom list column format the 'tomtom' list column contains data.frames with the following format: - name: name of query PWM - altname: alternate name of query PWM - match_name: name of matched PWM - match_altname: alt name of matched PWM - match_pval: p-value of match - match_eval: E-value of match - match_qval: q-value of match - match_offset: number of letters the query was offset from the target match - match_strand: whether the motif was found on input strand (+) or as reverse-complement (-) - db_name: database source of matched motif - match_motif: universalmotif object containing the PWM that was matched

Value

will return data.frame with input motifs & results for best match. 'tomtom' list column contains full tomtom data for each input motif. NOTE: if tomtom detects no matches for any input motif, currently will print a message & return NA values for 'tomtom', 'best_match_name', and 'best_match_motif'.

See Also

[runTomTom()]

Examples

tomtom_xml <- system.file("extdata", "tomtom.xml", package = "memes")
importTomTomXML(tomtom_xml)

snystrom/dremeR documentation built on Oct. 13, 2024, 10:48 p.m.