manhattan_plot: Create a Manhattan plot for the results of HiCcompare

View source: R/manhattan_plot.R

manhattan_plotR 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)

dozmorovlab/HiCcompare documentation built on Nov. 29, 2022, 9:58 a.m.