FreeHiC spikein

Add spikein to contact matrix.

FreeSpikeIn(
  contactBackground,
  contactSpikeInSignal,
  kernelSmooth = TRUE,
  bandwidth = 500000L
)

Arguments

contactBackground	The contact matrix. It can be matrixA matrix with columns (x, y, counts). data.frameA data.frame with columns (chr1, x, y, chr2, counts). listA list of matrix, where the matrix has columns (x, y, counts). where x stands for the first chromosome location, y stands for the second chromosome location and counts is the interaction counts.
contactSpikeInSignal	The spikein signal. It should has the exact same format as contactBackground
kernelSmooth	TRUE or FALSE. Whether to perform kernel smoothing.
bandwidth	The bandwidth used in the kernel smooth.

Value

A same format as contactBackground

Details

Spikein will add signals to the background. Also use Gaussian kernel smooth with bandwidth.

Examples

library(FreeHiCLite)

N <- 2000
Ns <- 200
maxBinX <- maxBinY <- 2000000L
maxCounts <- 10
binX <- sample(1:maxBinX, N, replace=TRUE)
binY <- sample(1:maxBinY, N, replace=TRUE)
counts <- sample(1:10, N, replace=TRUE)

kernelSmooth = TRUE
bandwidth = 50000L


## Matrix version
## matrix layout as x, y, counts

contacts <- matrix(0, N, 3)
contacts[,1] <- binX
contacts[,2] <- binY
contacts[,3] <- counts

spikeIn <- contacts[sample(1:N, Ns),]
hist(spikeIn[,3])

spikeIn[,3] <- spikeIn[,3] * sample(seq(0, 10, 0.5), Ns, replace=TRUE)
hist(spikeIn[,3])

res <- FreeSpikeIn(contacts, spikeIn, kernelSmooth = kernelSmooth, bandwidth = bandwidth)
head(res)
#>            x    y counts
#> [1,]  463789 1895      8
#> [2,]  524004 3068      5
#> [3,]  414539 3484     11
#> [4,] 1322176 3904      7
#> [5,]  694618 5505      6
#> [6,]  985692 6096     14

## List version
N2 = 3000
Ns2 = 300
binX2 <- sample(1:maxBinX, N2, replace=TRUE)
binY2 <- sample(1:maxBinY, N2, replace=TRUE)
counts2 <- sample(1:10, N2, replace=TRUE)

contacts2 <- matrix(0, N2, 3)
contacts2[,1] <- binX2
contacts2[,2] <- binY2
contacts2[,3] <- counts2

spikeIn2 <- contacts2[sample(1:N2, Ns2),]
spikeIn2[,3] <- spikeIn2[,3] * sample(seq(0, 10, 0.5), Ns2, replace=TRUE)

contactsBackgroup <- list('1_1' = contacts, '2_2' = contacts2)
spikeInlist <- list('1_1' = spikeIn, '2_2' = spikeIn2)

res <- FreeSpikeIn(contactsBackgroup, spikeInlist,
kernelSmooth = kernelSmooth, bandwidth = bandwidth)
str(res)
#> List of 2
#>  $ 1_1: int [1:2000, 1:3] 463789 524004 414539 1322176 694618 985692 1762793 547605 1975355 1684675 ...
#>   ..- attr(*, "dimnames")=List of 2
#>   .. ..$ : NULL
#>   .. ..$ : chr [1:3] "x" "y" "counts"
#>  $ 2_2: int [1:3000, 1:3] 1254932 394790 1227661 1510126 1185085 1984565 1779963 118297 10647 1443158 ...
#>   ..- attr(*, "dimnames")=List of 2
#>   .. ..$ : NULL
#>   .. ..$ : chr [1:3] "x" "y" "counts"

## Dataframe version

chr1 <- c(rep('1', N), rep('2', N2))
chr2 <- c(rep('1', N), rep('2', N2))

schr1 <- c(rep('1', Ns), rep('2', Ns2))
schr2 <- c(rep('1', Ns), rep('2', Ns2))

contactsAll <- rbind(contacts, contacts2)
spikeInAll <- rbind(spikeIn, spikeIn2)

contactsDf <- data.frame(chr1 = chr1, x = contactsAll[,1],
chr2 = chr2, y = contactsAll[,2], counts = contactsAll[,3])
spikeInDf <- data.frame(chr1 = schr1, x = spikeInAll[,1],
chr2 = schr2, y = spikeInAll[,2], counts = spikeInAll[,3])
res <- FreeSpikeIn(contactsDf, spikeInDf,
kernelSmooth = kernelSmooth, bandwidth = bandwidth)
head(res)
#>   chr1       x chr2    y counts
#> 1    1  463789    1 1895      8
#> 2    1  524004    1 3068      5
#> 3    1  414539    1 3484     11
#> 4    1 1322176    1 3904      7
#> 5    1  694618    1 5505     23
#> 6    1  985692    1 6096     14