inst/doc/sevenC.R

In sevenC: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs

## ---- eval = FALSE------------------------------------------------------------
#  # install.packages("BiocManager")
#  BiocManager::install("sevenC")

## ---- results = "hide", message = FALSE---------------------------------------
library(sevenC)

# load provided CTCF motifs in human genome
motifs <- motif.hg19.CTCF.chr22

# get motifs pairs
gi <- prepareCisPairs(motifs)

## ----eval = FALSE, echo = TRUE------------------------------------------------
#  
#  # use example ChIP-seq bigWig file
#  bigWigFile <- system.file("extdata", "GM12878_Stat1.chr22_1-30000000.bigWig",
#    package = "sevenC")
#  
#  # add ChIP-seq coverage and compute correaltion at motif pairs
#  gi <- addCor(gi, bigWigFile)

## ----eval = TRUE, echo = FALSE------------------------------------------------
# check if on windows to prevent bigWig reading errors from rtracklayer
if (.Platform$OS.type == 'windows') {
  # use motif data with ChIP-seq coverage
  motifs <- motif.hg19.CTCF.chr22.cov
  gi <- prepareCisPairs(motifs)
  gi <- addCovCor(gi)
  
} else {
  # use example ChIP-seq bigWig file
  bigWigFile <- system.file("extdata", "GM12878_Stat1.chr22_1-30000000.bigWig", 
    package = "sevenC")
  
  # add ChIP-seq coverage and compute correaltion at motif pairs
  gi <- addCor(gi, bigWigFile)
}

## -----------------------------------------------------------------------------
# predict looping interactions among all motif pairs
loops <- predLoops(gi)

## ---- results = "hide", message = FALSE---------------------------------------
library(sevenC)

# load provided CTCF motifs
motifs <- motif.hg19.CTCF.chr22

## -----------------------------------------------------------------------------
# use example ChIP-seq bigWig file
bigWigFile <- system.file("extdata", "GM12878_Stat1.chr22_1-30000000.bigWig", 
  package = "sevenC")

## ----eval = FALSE-------------------------------------------------------------
#  # read ChIP-seq coverage
#  motifs <- addCovToGR(motifs, bigWigFile)

## ----eval = TRUE, echo = FALSE------------------------------------------------
# check if OS is windows
if (.Platform$OS.type == 'windows') {
  motifs <- motif.hg19.CTCF.chr22.cov
} else {
  # read ChIP-seq coverage 
  motifs <- addCovToGR(motifs, bigWigFile)
}

## -----------------------------------------------------------------------------
motifs$chip

## -----------------------------------------------------------------------------
gi <- prepareCisPairs(motifs, maxDist = 10^6)

gi

## -----------------------------------------------------------------------------
# add ChIP-seq coverage and compute correaltion at motif pairs
gi <- addCovCor(gi)

## -----------------------------------------------------------------------------
loops <- predLoops(gi)

loops

## ---- results = "hide", message = FALSE---------------------------------------
library(GenomicInteractions)

# export to output file
export.bedpe(loops, "loop_interactions.bedpe", score = "pred")


## ----eval = FALSE, echo = TRUE------------------------------------------------
#  # load provided CTCF motifs
#  motifs <- motif.hg19.CTCF.chr22
#  
#  # use example ChIP-seq coverage file
#  bigWigFile <- system.file("extdata", "GM12878_Stat1.chr22_1-30000000.bigWig",
#    package = "sevenC")
#  
#  # add ChIP-seq coverage
#  motifs <- addCovToGR(motifs, bigWigFile)
#  
#  # build motif pairs
#  gi <- prepareCisPairs(motifs, maxDist = 10^6)
#  
#  # add correaltion of ChIP-signal
#  gi <- addCovCor(gi)

## ----eval = TRUE, echo = FALSE------------------------------------------------
# check if OS is windows
if (.Platform$OS.type == 'windows') {
  motifs <- motif.hg19.CTCF.chr22.cov
} else {
  # load provided CTCF motifs
  motifs <- motif.hg19.CTCF.chr22
  
  # use example ChIP-seq coverage file
  bigWigFile <- system.file("extdata", "GM12878_Stat1.chr22_1-30000000.bigWig", 
    package = "sevenC")
  
  # add ChIP-seq coverage
  motifs <- addCovToGR(motifs, bigWigFile)
}
  
gi <- prepareCisPairs(motifs, maxDist = 10^6)

# add correaltion of ChIP-signal
gi <- addCovCor(gi)

## ---- message = FALSE---------------------------------------------------------
# parse known loops
knownLoopFile <- system.file("extdata", 
  "GM12878_HiCCUPS.chr22_1-30000000.loop.txt", package = "sevenC")

knownLoops <- parseLoopsRao(knownLoopFile)

## -----------------------------------------------------------------------------
# add known loops
gi <- addInteractionSupport(gi, knownLoops)

## -----------------------------------------------------------------------------
fit <- glm(
  formula = loop ~ cor_chip + dist + strandOrientation, 
  data = mcols(gi), 
  family = binomial()
  )

## -----------------------------------------------------------------------------
# add predict loops
gi <- predLoops(
  gi,
  formula = loop ~ cor_chip + dist + strandOrientation,
  betas = coef(fit),
  cutoff = NULL
)

## -----------------------------------------------------------------------------
gi 

## ---- fig.width = 3, fig.height = 4-------------------------------------------
boxplot(gi$pred ~ gi$loop, 
        ylab = "Predicted interaction probability")


## -----------------------------------------------------------------------------
sessionInfo()