InputMatrixFormatted: InputMatrixFormatted: make the input data meet the format...
In rakarnik/MICC: Model based Interaction Calling from ChIA-PET data

Description Usage Arguments Value Author(s) See Also Examples

This function is used to make the input PET clusters meet the format requirements of MICC model

1	InputMatrixFormatted(data)

data

PET clusters. The input PET clusters should have 9 columns as: chromosome; start; end; chromosome; start; end; PET-count between two anchor regions; total PET-count in left anchor region; total PET-count in right anchor region

`cAB`	PET-count between two anchor regions
`cA`	Total PET-count in left anchor region
`cB`	Total PET-count in right anchor region
`distance`	genomic distance between two anchor regions, unit: kb; for inter-chromosomal PET clusters, distance="inf"

Chao He

MICC_1.0-package

library(MICC)

## Import data
data(TestData)

# format the data
data_formatted <- InputMatrixFormatted(TestData)

## The function is currently defined as
function (data) 
{
    x <- data
    cAB <- x[, 7]
    cA <- x[, 8]
    cB <- x[, 9]
    intra <- as.character(x[, 1]) == as.character(x[, 4])
    inter <- as.character(x[, 1]) != as.character(x[, 4])
    distance <- (x[, 5] + x[, 6] - x[, 3] - x[, 2])/2/1000
    distance[inter] <- Inf
    data_formatted <- list(cAB = cAB, cA = cA, cB = cB, distance = distance)
  }