expand_1D_features {HiCDCPlus} | R Documentation

## expand_1D_features

### Description

Expands 1D features on the regions metadata handle of each list element (e.g., `gi_list[[1]]@regions@elementMetadata`) to the to 2D metadata e.g., `mcols(gi_list[[1]])`). Two feature values corresponding to each anchor is summarized as a score using a vector valued function agg that takes two vector valued arguments of the same size and outputs a vector of the same size as the input vectors. This defaults to the `transform.vec` function outlined in (Carty et al., 2017). For efficient use of memory, using add/expand 1D features (see `?add_1D_features` and `expand_1D_features`) in sequence is recommended instead of using `add_2D_features` directly for each chromosome.

### Usage

    expand_1D_features(gi_list, chrs = NULL, features = NULL, agg = transform.vec)

### Arguments

`gi_list` | List of `GenomicInteractions` objects where each object named with chromosomes contains intra-chromosomal interaction information (see `?gi_list_validate` for a detailed explanation of valid `gi_list` instances).
`chrs` | a subset of chromosomes' e.g., c('chr21','chr22'). Defaults to all chromosomes in the `gi_list` instance.
`features` | features to be added. Defaults to all 1D features in elements of `gi_list[[1]]@regions@elementMetadata`
`agg` | any vector valued function with two data arguments: defaults to `transform.vec` described in HiC-DC (Carty et al., 2017).

### Value

a gi_list element with 2D features stored in metadata handle (i.e., `mcols(gi)`).

### Examples

    df<-data.frame(chr='chr9',start=seq(1e6,10e6,1e6),end=seq(2e6,11e6,1e6))
    gi_list<-generate_df_gi_list(df)
    feats<-data.frame(chr='chr9',start=seq(1e6,10e6,1e6),gc=runif(10))
    gi_list<-add_1D_features(gi_list,feats)
    gi_list<-expand_1D_features(gi_list)

[Package HiCDCPlus version 1.0.0 Index]