topDirs {multiHiCcompare} | R Documentation |
Filter results of multiHiCcompare
topDirs(hicexp, logfc_cutoff = 1, logcpm_cutoff = 1, p.adj_cutoff = 0.01, D_cutoff = 1, alpha = 0.05, return_df = "pairedbed")
hicexp |
A hicexp object which has been compared. |
logfc_cutoff |
The logFC value you wish to filter by. Defaults to 1. |
logcpm_cutoff |
The logCPM cutoff you wish to filter by. Defaults to 1. |
p.adj_cutoff |
The adjusted p-value cutoff you wish to filter by. Defaults to 0.01. |
D_cutoff |
The distance cutoff you wish to filter by. Interactions with a D < D_cutoff will be filtered. Defaults to 1. |
alpha |
The p-value cutoff for determining the count of number of times a region is significant. Used to calculate the number of times a region was detected as significantly interacting. Defaults to 0.05. |
return_df |
The format for the data.frame returned by the function. Options are "bed" and "pairedbed". |
This function is meant to filter the results of multiHiCcompare. The top differentially interacting regions (DIRs) can be returned by using this function. When the return_df = "bed" option is set the resulting data.frame can be input into the plot_pvals or plot_counts functions to visualize the top DIRs.
A data.table containing the filtered results.
data('hicexp_diff') topDirs(hicexp_diff)