find_ep_coenrichment {spatzie} | R Documentation |
Identifies co-enriched pairs of motifs in enhancer-promoter interactions selected from a data frame of general genomic interactions.
If identify_ep
: Promoters and enhancers are identified
using genomic annotations, where anchors close to promoter annotations
(within 2500 base pairs) are considered promoters and all other anchors are
considered gene-distal enhancers. Only interactions in
int_raw_data
between promoters and enhancers are used for motif
co-enrichment analysis.
If !identify_ep
: Instead of automatically identifying
promoters and enhancers based on genomic annotations, all interactions
in int_raw_data
must be preprocessed in a way that anchor 1 contains
promoters and anchor 2 contains enhancers. Motif
co-enrichment analysis is performed under this assumption.
Calls functions scan_motifs
, filter_motifs
,
and anchor_pair_enrich
internally.
find_ep_coenrichment( int_raw_data, motifs_file, motifs_file_matrix_format = c("pfm", "ppm", "pwm"), genome_id = c("hg38", "hg19", "mm9", "mm10"), identify_ep = TRUE, cooccurrence_method = c("count", "score", "match"), filter_threshold = 0.4 )
int_raw_data |
a
| ||||||||||||
motifs_file |
JASPAR format matrix file containing multiple motifs to scan for, gz-zipped files allowed | ||||||||||||
motifs_file_matrix_format |
type of position-specific scoring matrices
in
| ||||||||||||
genome_id |
ID of genome assembly interactions in | ||||||||||||
identify_ep |
logical, set | ||||||||||||
cooccurrence_method |
method for co-occurrence, valid options include:
See | ||||||||||||
filter_threshold |
fraction of interactions that should contain a
motif for a motif to be considered, see |
a list with the following items:
int_data |
GenomicInteractions object;
promoter-enhancer interactions |
int_data_motifs : | interactionData object; return value of
scan_motifs |
filtered_int_data_motifs : | interactionData object;
return value of filter_motifs |
annotation_pie_chart : | ggplot2 plot; return value of
plotInteractionAnnotations |
motif_cooccurrence : | interactionData object; return
value of anchor_pair_enrich
|
Jennifer Hammelman
Konstantin Krismer
## Not run: interactions_file <- system.file("extdata/yy1_interactions.bedpe.gz", package = "spatzie") motifs_file <- system.file("extdata/motifs_subset.txt.gz", package = "spatzie") df <- read.table(gzfile(interactions_file), header = TRUE, sep = "\t") res <- find_ep_coenrichment(df, motifs_file, motifs_file_matrix_format = "pfm", genome_id = "mm10") ## End(Not run)