manhattan_plot {HiCcompare} | R Documentation

## Create a Manhattan plot for the results of HiCcompare

### Description

Create a Manhattan plot for the results of HiCcompare

### Usage

    manhattan_plot(hic.table, adj.p = TRUE, alpha = 0.05,
      return_df = FALSE)

### Arguments

`hic.table` | a hic.table object that has been normalized and had differences detected.
`adj.p` | Logical, should the adjusted p-value be used (TRUE) of the raw p-value (FALSE)?
`alpha` | The alpha level for calling a p-value significant.
`return_df` | Logical, should the data.frame built to be used for plotting be returned? If TRUE then the data.frame will be returned and the plot will only be printed.

### Details

This function will produce a manhattan plot of the results of hic_compare(). Can be used to display which regions around found to be significantly different on the linear genome.

### Value

A manhattan plot.

### Examples

    # Create hic.table object using included Hi-C data in
    # sparse upper triangular matrix format
    data('HMEC.chr22')
    data('NHEK.chr22')
    hic.table <- create.hic.table(HMEC.chr22, NHEK.chr22, chr = 'chr22')
    # Plug hic.table into hic_loess()
    result <- hic_loess(hic.table, Plot = TRUE)
    # perform difference detection
    diff.result <- hic_compare(result, Plot = TRUE)
    # make manhattan plot
    manhattan_plot(diff.result)

[Package HiCcompare version 1.10.0 Index]