| Title: | Clusters of Colocalized Sequences |
|---|---|
| Description: | Also abbreviates to "CCSeq". Finds clusters of colocalized sequences in .bed annotation files up to a specified cut-off distance. Two sequences are colocalized if they are within the cut-off distance of each other, and clusters are sets of sequences where each sequence is colocalized to at least one other sequence in the cluster. For a set of .bed annotation tables provided in a list along with a cut-off distance, the program will output a file containing the locations of each cluster. Annotated .bed files are from the 'pwmscan' application at <https://ccg.epfl.ch/pwmtools/pwmscan.php>. Personal machines might crash or take excessively long depending on the number of annotated sequences in each file and whether chromsearch() or gensearch() is used. |
| Authors: | Stefan Golas [cre, aut] |
| Maintainer: | Stefan Golas <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 0.2.0 |
| Built: | 2024-10-31 16:32:53 UTC |
| Source: | https://github.com/cran/colocalized |
Search a single chromosome for clusters of TF binding sequences. Example produces a null result, test the same complex on "chr9" for a positive reading.
chromsearch(choose, n, chrom)chromsearch(choose, n, chrom)
choose |
List of .bed tables |
n |
Cut-off distance between colocalized sequences |
chrom |
Chromosome to be searched given as e.g. "chr19" |
A table containing the addresses (as one dimensional intervals) of the members of every cluster, with some annotation data.
complex<-list(nfkb1,nfkb2,relb) chromsearch(complex,150,"chrY")complex<-list(nfkb1,nfkb2,relb) chromsearch(complex,150,"chrY")
Searches for clusters of colocalized transcription factor (TF) binding sequences.
colocalized(choose,chr,n) searches for instances where the sequences from each
table element in choose are colocalized to within a cut-off distance.
colocalized(choose, chr, n, cores)colocalized(choose, chr, n, cores)
choose |
List of .bed tables |
chr |
Chromosome |
n |
The cut-off distance |
cores |
Number of cores for parallel processing. Leaving this blank causes the program to use default (series) processing |
Table of clusters found in chr
complex<-list(nfkb1,nfkb2,relb) colocalized(complex,"chrY",150)complex<-list(nfkb1,nfkb2,relb) colocalized(complex,"chrY",150)
Search one chromosome for clusters using default non-parallel processing.
colocalized_sequential(choose, chr, n)colocalized_sequential(choose, chr, n)
choose |
List of .bed tables |
chr |
Chromosome to be searched given as e.g. "chr19" |
n |
Cut-off distance between colocalized sequences |
Table containing the addresses (as one dimensional intervals) of the members of every cluster, with some annotation data.
complex<-list(nfkb1,nfkb2,relb) colocalized_sequential(complex,"chrY",150)complex<-list(nfkb1,nfkb2,relb) colocalized_sequential(complex,"chrY",150)
Wrapper for colocalized that searches every chromosome shared
between the given .bed files.
ColocalizedFullSearch(choose, n, cores)ColocalizedFullSearch(choose, n, cores)
choose |
List of .bed tables |
n |
The cut-off distance |
cores |
Number of cores for parallel processing. Leaving this blank causes the program to use default (series) processing |
List of lists of each cluster found in each chromosome.
Search the whole genome for clusters of colocalized TF binding sequences.
gensearch(choose, n, cores)gensearch(choose, n, cores)
choose |
List of .bed tables |
n |
The cut-off distance |
cores |
Number of cores for parallel processing. Leaving this blank causes the program to use default (series) processing |
Table containing the addresses (as one dimensional intervals) of the members of every cluster, with some annotation data.
nfkb1
nfkb1 nfkb1nfkb1 nfkb1
A dataframe with 230505 rows and 8 columns
Stefan Golas
https://ccg.epfl.ch/pwmtools/pwmscan.php
https://ccg.epfl.ch/pwmtools/pwmscan.php
nfkb2
nfkb2 nfkb2nfkb2 nfkb2
A dataframe with 1901 rows and 8 columns
Stefan Golas
https://ccg.epfl.ch/pwmtools/pwmscan.php
https://ccg.epfl.ch/pwmtools/pwmscan.php
Create a colocalization matrix
onedim_dist(bed1, bed2, n)onedim_dist(bed1, bed2, n)
bed1 |
A .bed table |
bed2 |
A .bed table |
n |
The cut-off distance |
A colocalization matrix whose dimensions are the number of rows in
bed1 by the number of rows in bed2. Entry i,j is a 1 if the ith
sequence in bed1 is within the cut-off distance of the jth sequence
in bed2, and 0 otherwise.
chr<-"chrY" onedim_dist(nfkb1[which(nfkb1[,1]==chr),],nfkb2[which(nfkb2[,1]==chr),],150)chr<-"chrY" onedim_dist(nfkb1[which(nfkb1[,1]==chr),],nfkb2[which(nfkb2[,1]==chr),],150)
relb
relb relbrelb relb
A dataframe with 1448 rows and 8 columns
Stefan Golas
https://ccg.epfl.ch/pwmtools/pwmscan.php
https://ccg.epfl.ch/pwmtools/pwmscan.php