Nothing
## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
cache = TRUE,
eval = TRUE
);
## ---- warning = FALSE---------------------------------------------------------
library(chicane);
# example BAM file, baits, and restriction fragments
bam <- system.file('extdata', 'Bre80_2q35.bam', package = 'chicane');
baits <- system.file('extdata', '2q35.bed', package = 'chicane');
fragments <- system.file('extdata', 'GRCh38_HindIII_chr2.bed.gz', package = 'chicane'); # HindIII fragments on chromosome 2
if( bedtools.installed() ) {
chicane.results <- chicane(
bam = bam,
baits = baits,
fragments = fragments
);
print( chicane.results[ 1:10 ] );
}
## ---- warning = FALSE---------------------------------------------------------
if( bedtools.installed() ) {
interaction.data <- prepare.data(
bam = bam,
baits = baits,
fragments = fragments
);
}
## -----------------------------------------------------------------------------
if( bedtools.installed() ) print(interaction.data);
## ---- warning = FALSE, run = FALSE--------------------------------------------
if( bedtools.installed() ) {
file.name <- tempfile('interaction_data');
write.table(interaction.data, file.name, row.names = FALSE);
chicane.results <- chicane(interactions = file.name);
}
## -----------------------------------------------------------------------------
data(bre80);
adjusted.results <- chicane(
interactions = bre80,
adjustment.terms = 'target.chr'
);
print( adjusted.results[ 1:5 ] );
## ---- warning = FALSE, run = FALSE, eval = FALSE------------------------------
# if( bedtools.installed() ) {
# create.locus.plot(
# genome = 'hg38',
# chr = 'chr2', start = 111100000, end = 112200000,
# gene.data = '/path/to/gene_data.gtf',
# genomic.features = '/path/to/baitmap.bed',
# feature.name = 'baits',
# interaction.data = '/path/to/interaction_calls.txt',
# file.name = '/path/to/locus_plot.pdf'
# );
# }
## ---- warning = FALSE, run = FALSE, eval = FALSE------------------------------
# if( bedtools.installed() ) {
#
# # initial prep of interactions data table
# interaction.data <- prepare.data(
# bam = list.files('data/bams/T47D', pattern = '.bam', full.names = TRUE),
# baits = 'data/captured_fragments/T47D/Baxter_captured_fragments.bed',
# fragments = 'data/GRCh38_HindIII_fragments.bed'
# );
#
# # save interactions data table
# file.name <- tempfile('interaction_data');
# write.table(interaction.data, file.name, row.names = FALSE);
#
# # run interaction calling and save model fit plots and statistics
# chicane.results <- chicane(
# interactions = file.name,
# interim.data.dir = 'graphs/T47D/model_fits'
# );
#
# # save full interaction calls table
# write.table(
# chicane.results,
# file = 'data/chicane/T47D/interaction_calls.txt',
# row.names = FALSE,
# quote = FALSE,
# sep = '\t'
# );
#
# # filter for significant only and save these results separately
# significant.results <- chicane.results[q.value < 0.05]
#
# write.table(
# significant.results,
# file = 'data/chicane/T47D/interaction_calls_significant.txt',
# row.names = FALSE,
# quote = FALSE,
# sep = '\t'
# );
#
# }
## ---- warning = FALSE, run = FALSE, eval = FALSE------------------------------
# if( bedtools.installed() ) {
#
# # calculate proportions by interaction type
# total <- nrow(significant.results);
# trans.prop <- sum(is.na(significant.results$distance))/total;
# cis.prop <- sum(!is.na(significant.results$distance))/total;
# b2b.prop <- sum(significant.results$bait.to.bait)/total;
# int.data <- c('trans' = trans.prop, 'cis' = cis.prop, 'bait.to.bait' = b2b.prop);
# print(int.data);
#
# # get number of interactions by distance bins
# binned.data <- NULL;
#
# distance.bins <- list(
# "0-10kbp" = c(0, 1e4),
# "10-100kbp" = c(1e4, 1e5),
# "100kbp-1Mbp" = c(1e5, 1e6),
# "1-10Mbp" = c(1e6, 1e7),
# "10-100Mbp" = c(1e7, 1e8),
# "100-1000Mbp" = c(1e8, 1e9)
# );
#
# for(dist.i in names(distance.bins)){
# bin.sum <- length(which(significant.results$distance >= distance.bins[[dist.i]][1] & significant.results$distance < distance.bins[[dist.i]][2]));
# binned.data <- cbind(binned.data, bin.sum);
# }
#
# colnames(binned.data) <- names(distance.bins);
# print(binned.data);
#
# }
## ---- warning = FALSE, run = FALSE, eval = FALSE------------------------------
# if( bedtools.installed() ) {
#
# # make a browser compatible file from significant interactions
# browser.file <- tempfile('significant_calls_standard.txt')
# convert.standard.format(
# chicane.results = 'data/chicane/T47D/interaction_calls_significant.txt',
# file.name = browser.file
# );
#
# }
## ---- warning = FALSE, run = FALSE, eval = FALSE------------------------------
# if( bedtools.installed() ) {
#
# # set genome annotation file
# gene.ann <- system.file('extdata', 'gencode_2q35.gtf', package = 'chicane');
#
# # generate 2q35 locus plot
# create.locus.plot(
# genome = 'hg38',
# chr = 'chr2',
# start = 216600000,
# end = 217140000,
# gene.data = gene.ann,
# genomic.features = 'data/captured_fragments/T47D/Baxter_captured_fragments.bed',
# feature.name = 'baits',
# interaction.data = 'data/chicane/T47D/interaction_calls.txt',
# file.name = 'graphs/T47D/2q35.pdf'
# );
#
# }
## -----------------------------------------------------------------------------
sessionInfo();
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