establish_bijection1d {idr2d} | R Documentation

## 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)

[Package idr2d version 1.2.2 Index]