establish_bijection1d: Finds One-to-One Correspondence between Peaks from Replicate...

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

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

Description

This method establishes a bijective assignment between peaks from replicate 1 and 2. A peak in replicate 1 is assigned to a peak in replicate 2 if and only if (1) they overlap (or the gap between the peaks is less than or equal to max_gap), and (2) there is no other peak in replicate 2 that overlaps with the peak in replicate 1 and has a lower ambiguity resolution value.

Usage

establish_bijection1d(
  rep1_df,
  rep2_df,
  ambiguity_resolution_method = c("overlap", "midpoint", "value"),
  max_gap = -1L
)

Arguments

rep1_df	data frame of observations (i.e., genomic peaks) of replicate 1, with at least the following columns (position of columns matter, column names are irrelevant): column 1: chr character; genomic location of peak - chromosome (e.g., "chr3") column 2: start integer; genomic location of peak - start coordinate column 3: end integer; genomic location of peak - end coordinate column 4: value numeric; p-value, FDR, or heuristic used to rank the interactions
rep2_df	data frame of observations (i.e., genomic peaks) of replicate 2, with the following columns (position of columns matter, column names are irrelevant): column 1: chr character; genomic location of peak - chromosome (e.g., "chr3") column 2: start integer; genomic location of peak - start coordinate column 3: end integer; genomic location of peak - end coordinate column 4: value numeric; p-value, FDR, or heuristic used to rank the interactions
ambiguity_resolution_method	defines how ambiguous assignments (when one interaction in replicate 1 overlaps with multiple interactions in replicate 2 or vice versa) are resolved. Available methods: "value" interactions are prioritized by ascending or descending value column (see sorting_direction), e.g., if two interactions in replicate 1 overlap with one interaction in replicate 2, the interaction from replicate 1 is chosen which has a lower (if sorting_direction is "ascending") or higher (if "descending") value "overlap" the interaction pair is chosen which has the highest relative overlap, i.e., overlap in nucleotides of replicate 1 interaction anchor A and replicate 2 interaction anchor A, plus replicate 1 interaction anchor B and replicate 2 interaction anchor B, normalized by their lengths "midpoint" the interaction pair is chosen which has the smallest distance between their anchor midpoints, i.e., distance from midpoint of replicate 1 interaction anchor A to midpoint of replicate 2 interaction anchor A, plus distance from midpoint of replicate 1 interaction anchor B to midpoint of replicate 2 interaction anchor B
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

Data frames rep1_df and rep2_df with the following columns:

column 1:	chr	character; genomic location of peak - chromosome (e.g., "chr3")
column 2:	start	integer; genomic location of peak - start coordinate
column 3:	end	integer; genomic location of peak - end coordinate
column 4:	value	numeric; p-value, FDR, or heuristic used to rank the peaks
column 5:	rep_value	numeric; value of corresponding replicate peak. If no corresponding peak was found, rep_value is set to NA.
column 6:	rank	integer; rank of the peak, established by value column, ascending order
column 7:	rep_rank	integer; rank of corresponding replicate peak. If no corresponding peak was found, rep_rank is set to NA.
column 8:	idx	integer; peak index, primary key
column 9:	rep_idx	integer; specifies the index of the corresponding peak in the other replicate (foreign key). If no corresponding peak was found, rep_idx is set to NA.

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_bijection1d(rep1_df, rep2_df)

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