| Type: | Package |
| Title: | Clusters of Colocalized Sequences |
| Version: | 0.2.0 |
| 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. |
| License: | MIT + file LICENSE |
| Encoding: | UTF-8 |
| LazyData: | true |
| RoxygenNote: | 6.1.1.9000 |
| Depends: | R (≥ 3.0.0) |
| Imports: | foreach, doParallel, purrr, utils |
| NeedsCompilation: | no |
| Packaged: | 2019-10-18 00:45:17 UTC; Stefan |
| Author: | Stefan Golas [cre, aut] |
| Maintainer: | Stefan Golas <stefanmgolas@gmail.com> |
| Repository: | CRAN |
| Date/Publication: | 2019-10-18 21:20:12 UTC |
Colocalized full search.
Description
Wrapper for colocalized that searches every chromosome shared
between the given .bed files.
Usage
ColocalizedFullSearch(choose, n, cores)
Arguments
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 |
Value
List of lists of each cluster found in each chromosome.
Search one chromsome
Description
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.
Usage
chromsearch(choose, n, chrom)
Arguments
choose |
List of .bed tables |
n |
Cut-off distance between colocalized sequences |
chrom |
Chromosome to be searched given as e.g. "chr19" |
Value
A table containing the addresses (as one dimensional intervals) of the members of every cluster, with some annotation data.
Examples
complex<-list(nfkb1,nfkb2,relb)
chromsearch(complex,150,"chrY")
Colocalized cluster search.
Description
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.
Usage
colocalized(choose, chr, n, cores)
Arguments
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 |
Value
Table of clusters found in chr
Examples
complex<-list(nfkb1,nfkb2,relb)
colocalized(complex,"chrY",150)
Sequential cluster search
Description
Search one chromosome for clusters using default non-parallel processing.
Usage
colocalized_sequential(choose, chr, n)
Arguments
choose |
List of .bed tables |
chr |
Chromosome to be searched given as e.g. "chr19" |
n |
Cut-off distance between colocalized sequences |
Value
Table containing the addresses (as one dimensional intervals) of the members of every cluster, with some annotation data.
Examples
complex<-list(nfkb1,nfkb2,relb)
colocalized_sequential(complex,"chrY",150)
Whole genome search.
Description
Search the whole genome for clusters of colocalized TF binding sequences.
Usage
gensearch(choose, n, cores)
Arguments
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 |
Value
Table containing the addresses (as one dimensional intervals) of the members of every cluster, with some annotation data.
NFKB1 bed file
Description
nfkb1
Usage
nfkb1
nfkb1
Format
A dataframe with 230505 rows and 8 columns
Author(s)
Stefan Golas
Source
https://ccg.epfl.ch/pwmtools/pwmscan.php
https://ccg.epfl.ch/pwmtools/pwmscan.php
NFKB2 bed file
Description
nfkb2
Usage
nfkb2
nfkb2
Format
A dataframe with 1901 rows and 8 columns
Author(s)
Stefan Golas
Source
https://ccg.epfl.ch/pwmtools/pwmscan.php
https://ccg.epfl.ch/pwmtools/pwmscan.php
Create a colocalization matrix
Description
Create a colocalization matrix
Usage
onedim_dist(bed1, bed2, n)
Arguments
bed1 |
A .bed table |
bed2 |
A .bed table |
n |
The cut-off distance |
Value
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.
Examples
chr<-"chrY"
onedim_dist(nfkb1[which(nfkb1[,1]==chr),],nfkb2[which(nfkb2[,1]==chr),],150)
RELB bed file
Description
relb
Usage
relb
relb
Format
A dataframe with 1448 rows and 8 columns
Author(s)
Stefan Golas