establish_bijection: Finds One-to-One Correspondence between Peaks or interactions...

In kkrismer/idr2d: Irreproducible Discovery Rate for Genomic Interactions Data

Finds One-to-One Correspondence between Peaks or interactions from Replicate 1 and 2

Description

This method establishes a bijective assignment between observations (genomic peaks in case of ChIP-seq, genomic interactions in case of ChIA-PET, HiChIP, and Hi-C) from replicate 1 and 2. An observation in replicate 1 is assigned to an observation in replicate 2 if and only if (1) the observation loci in both replicates overlap (or the gap between them is less than or equal to max_gap), and (2) there is no other observation in replicate 2 that overlaps with the observation in replicate 1 and has a lower ambiguity resolution value.

Usage

establish_bijection(
  rep1_df,
  rep2_df,
  analysis_type = c("IDR1D", "IDR2D"),
  ambiguity_resolution_method = c("overlap", "midpoint", "value"),
  max_gap = -1L
)

Arguments

rep1_df	data frame of observations (i.e., genomic peaks or genomic interactions) of replicate 1. If analysis_type is IDR1D, the columns of rep1_df are described in establish_bijection1d, otherwise in establish_bijection2d
rep2_df	data frame of observations (i.e., genomic peaks or genomic interactions) of replicate 2. Same columns as rep1_df.
analysis_type	"IDR2D" for genomic interaction data sets, "IDR1D" for genomic peak data sets
ambiguity_resolution_method	defines how ambiguous assignments (when one interaction or peak in replicate 1 overlaps with multiple interactions or peaks in replicate 2 or vice versa) are resolved. For available methods, see establish_overlap1d or establish_overlap2d, respectively.
max_gap	integer; maximum gap in nucleotides allowed between two anchors for them to be considered as overlapping (defaults to -1, i.e., overlapping anchors)

Value

See establish_bijection1d or establish_bijection2d, respectively.

Examples

rep1_df <- idr2d:::chipseq$rep1_df
rep1_df$value <- preprocess(rep1_df$value, "log")

rep2_df <- idr2d:::chipseq$rep2_df
rep2_df$value <- preprocess(rep2_df$value, "log")

mapping <- establish_bijection(rep1_df, rep2_df, analysis_type = "IDR1D")

kkrismer/idr2d documentation built on Feb. 7, 2024, 2:23 p.m.