FIRE_plot: FIREcaller: an R package for detecting frequently interacting...

In yycunc/FIREcaller: FIREcaller: an R package for detecting frequently interacting regions from Hi-C data

FIREcaller: an R package for detecting frequently interacting regions from Hi-C data

Description

This function FIRE_plot() in the FIREcaller package (a user-friendly R package for detecting FIREs from Hi-C data), Visualized the FIREcaller FIRE and superFIRE results for a sample and plots them in a circos plot by utilizing the circlize function in R, with the allowance of 3 additional annotation data.

Usage

FIRE_plot(FIRE="",prefix="", gb=c('hg19','gb38','mm9','mm10'),chr.list=c('chr1','chr2',...),outname="",anno_list=c(""),color=c('red','darkgreen','orange','blue','purple'))

Arguments

FIRE	The name of the FIREcaller output for identifying the FIREs. With default parameters, this file is 'FIRE_ANALYSIS_40000_200000_poisson.txt'.
prefix	The prefix of the sample used in the "prefix.list" option in the FIREcaller function.
gb	The name of the genome build for the ideogram. Default is hg19 but options include gb38,mm9, and mm10
chr.list	The list of chromosomes visualized
outname	A string of the name for a JPEG file of the circos plot is desired. If a jpeg is not desired, set to NA.
anno_list	The optional list of files (up to 3) to also include into the circos plot, such as TADs, enhancers, or super-enhancers, with each file containing 3 columns (chr/start/end position)
color	The optional list of colors for the tracks if the default is not preferred. The number of colors specified needs to be >= the number of annotations

Details

The process includes Quantile Normalization (if number of samples > 1 and qqnorm=TRUE), and highlighting significant Fire Scores, and calculating the Super Fires.

Value

Two sets of files will be returned. The total number of files outputted are 1+ (number of prefixes/samples):

• Fire: a single text file is outputted for all the samples and all chromosomes.This file contains the Fire Score, associated ln(pvalue), and an indicator if the region is a FIRE or not with I(pvalues > -ln(0.05)).

• SuperFire: a text file for each sample with a list of Super Fires and corresponding -log10(pvalue).

Note

The input for this function should be same format as the output of the complement function find_cis_inter()

Author(s)

Crowley, Cheynna Anne <[e-mail]>, Yuchen Yang <[e-mail]>, Ming Hu <[e-mail]>, Yun Li <[e-mail]>

References

Cheynna Crowley, Yuchen Yang, Ming Hu, Yun Li. FIREcaller: an R package for detecting frequently interacting regions from Hi-C data

See Also

Paper: https://doi.org/10.1016/j.celrep.2016.10.061 bioarxiv: https://doi.org/10.1101/619288

Examples

# the name of the file for the  normalized cis-interactions
norm_file<-"Hippo_norm.txt"

# define the alpha cut off for a significant p-value
alpha<-0.05

#specify if quantile normalization across samples are needed (qqnorm=TRUE). If the normalization procedure does within and across, then set qqnorm=FALSE.
qqnorm<-FALSE

#option for user to specify an outname for the FIRE analysis. Defaulted at FIRE_ANALYSIS.txt
outname='FIRE_ANALYSIS.txt'

# run the function
FIRE_calc(norm_file, alpha=0.05,qqnorm=TRUE,outname='FIRE_ANALYSIS.txt')

yycunc/FIREcaller documentation built on Nov. 13, 2022, 7:49 p.m.