makeGInteractionsFromDataFrame: Convert DataFrames to GInteraction objects

In EricSDavis/hictoolsr: An R Package for Hi-C Data Analysis

Convert DataFrames to GInteraction objects

Description

makeGInteractionsFromDataFrame takes a paired-interaction (i.e. BEDPE) formatted data-frame-like object and converts it to a GInteractions object. For convenience, as_ginteractions() can be used as an alias.

Usage

makeGInteractionsFromDataFrame(
  df,
  keep.extra.columns = TRUE,
  starts.in.df.are.0based = FALSE
)

as_ginteractions(
  df,
  keep.extra.columns = TRUE,
  starts.in.df.are.0based = FALSE
)

Arguments

df	A data.table, data.frame, or DataFrame object. Assumes that the first 6 colummns are in the format chr1, start1, end1 and chr2, start2, end2, representing each pair of interactions.
keep.extra.columns	TRUE or FALSE (the default). If TRUE, the columns in df that are not used to form the genomic ranges of the returned GRanges object are then returned as metadata columns on the object. Otherwise, they are ignored. If df has a width column, then it's always ignored.
starts.in.df.are.0based	TRUE or FALSE (the default). If TRUE, then the start positions of the genomic ranges in df are considered to be 0-based and are converted to 1-based in the returned GRanges object. This feature is intended to make it more convenient to handle input that contains data obtained from resources using the "0-based start" convention. A notorious example of such resource is the UCSC Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables).

Value

GInteraction object

Examples

## data.frame
df <- data.frame(chr1 = "chr1", x1 = 10000, x2 = 20000,
                 chr2 = "chr1", y1 = 30000, y2 = 40000)
makeGInteractionsFromDataFrame(df)

## data.table
df <- data.table(chr1 = "chr1", x1 = 10000, x2 = 20000,
                 chr2 = "chr1", y1 = 30000, y2 = 40000)
makeGInteractionsFromDataFrame(df)

## DataFrame
df <- DataFrame(chr1 = "chr1", x1 = 10000, x2 = 20000,
                chr2 = "chr1", y1 = 30000, y2 = 40000)
makeGInteractionsFromDataFrame(df)

## Alias
df <- data.frame(chr1 = "chr1", x1 = 10000, x2 = 20000,
                 chr2 = "chr1", y1 = 30000, y2 = 40000,
                 pval = 0.05, dist = 10000)
as_ginteractions(df)

## Additional metadata
df <- data.frame(chr1 = "chr1", x1 = 10000, x2 = 20000,
                 chr2 = "chr1", y1 = 30000, y2 = 40000,
                 pval = 0.05, dist = 10000)
as_ginteractions(df)

## Remove additional metadata
as_ginteractions(df, keep.extra.columns = F)

## Add 1 to starts (for 0-based programs)
as_ginteractions(df, starts.in.df.are.0based = T)

## Bad usage
df <- data.frame(chr1 = "chr1", x1 = 10000, x2 = 20000,
                 chr2 = "chr1", y1 = 30000)
makeGInteractionsFromDataFrame(df)

EricSDavis/hictoolsr documentation built on Sept. 4, 2022, 12:36 a.m.