add_1D_features {HiCDCPlus} | R Documentation

## add_1D_features

### Description

Adds 1D features to the gi_list instance. If any bin on gi_list overlaps with multiple feature records, feature values are aggregated for the bin according to the vector valued function agg (e.g., sum, mean)

### Usage

    add_1D_features(gi_list, df, chrs = NULL, features = NULL, agg = mean)

### Arguments

`gi_list` | List of `GenomicInteractions` objects where each object named with chromosomes contains intrachromosomal interaction information (see `?gi_list_validate` for a detailed explanation of valid `gi_list` instances).
`df` | DataFrame with columns named 'chr', and'start' and features to be added with their respective names.
`chrs` | a subset of chromosomes' e.g., c('chr21','chr22'). Defaults to all chromosomes specified in the data frame `df`.
`features` | features to be added. Needs to be a subset of `colnames(df)`. Defaults to all columns in `df` other than 'chr','start',and 'end'.
`agg` | any vector valued function with one data argument: defaults to `mean`.

### Value

a gi_list instance with 1D features stored in regions metadata handle of each list element (e.g., `gi_list[[1]]@regions@elementMetadata`) in the instance

### 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)

[Package HiCDCPlus version 1.0.0 Index]