direct_gene_cna {iGC} | R Documentation

## Load the existed CNA gain/loss based on gene location.

### Description

This function aims to complement `create_gene_cna`. Instead of mapping CNA records onto genes by genome reference, it reads the existed column containing the gene each CNA lies on. Two functions share the same interface but they have different requirement for the `read_fun` implementation.

### Usage

    direct_gene_cna(sample_desc, gain_threshold = log2(2.5) - 1,
      loss_threshold = log2(1.5) - 1, read_fun = NULL, progress = TRUE,
      progress_width = 48, parallel = FALSE, ...)

### Arguments

`sample_desc` | data.table object created by create_sample_desc.
`gain_threshold` | CNA expression above this will be considered as gain region. By default \log_2{2.5} - 1
`loss_threshold` | CNA expression below this will be considered as loss region. By default \log_2{1.5} - 1
`read_fun` | Custom reader function, see its own section for more detail.
`progress` | Whether to display a progress bar. By default `TRUE`.
`progress_width` | The text width of the shown progress bar. By default is 48 chars wide.
`parallel` | Enable parallelism by plyr. One has to specify a parallel engine beforehand. See example for more information.
`...` | Arguments passed to the custom reader function specified in `read_fun`.

### Value

data.table of CNA gain/loss on each gene region for all samples, whose rows represent regions of genes and columns are sample names. First column `GENE` contains the corresponding gene names.

### Custom reader function

Similar to that of create_gene_cna, the reader function takes the filepath as the first argument. It will return a data.table with at least two columns: `GENE` and `Segment_Mean` of type `character` and `numeric` respectively.

### See Also

`create_gene_cna`

### Examples

    require(data.table)

    ## Create a CNA dataset that has been already mapped onto gene regions

    cna_geo_list = list(
        sample_A = data.table(
            GENE = c("TP53", "BRCA2"),
            Segment_Mean = c(1.05, -2.03)
        ),
        sample_B = data.table(
            GENE = c("TP53", "BRCA2", "NDPH1"),
            Segment_Mean = c(0.38, -1.71, 2.6)
        )
    )
    sample_desc <- data.table(
        Sample = paste("sample", c("A", "B"), sep = "_")
    )
    sample_desc$CNA_filepath <- sample_desc$Sample

    ## Example code for reading

    read_cna_geo <- function(pth) {
        # For demonstration, file reading silently redirects
        # to list lookup
        cna_geo_list[[pth]]
    }
    gene_cna <- direct_gene_cna(
        sample_desc,
        read_fun = read_cna_geo, progress = FALSE
    )
    gene_cna

[Package iGC version 1.12.0 Index]