create_gene_exp {iGC} | R Documentation

## Create an joint gene expression table of all samples

### Description

The function reads in all gene expression data given by the sample description `sample_desc` and return a joint expression table of all samples.

### Usage

    create_gene_exp(sample_desc, read_fun = NULL, progress = TRUE,
      progress_width = 48, ...)

### Arguments

`sample_desc` | data.table object created by create_sample_desc.
`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.
`...` | Arguments passed to the custom reader function specified in `read_fun`.

### Details

By default it assumes the data to be of TCGA level 3 file format. However, nearly all real world data fail to have the same format as TCGA. In this case, one needs to tell the function how to parse the data by implementing a custom reader function that accepts the filepath as the first argument. See Detail section for full specification. The function naively concatenates all return expression as if all gene expressions are stated in the same gene order as columns in a new data.table.

### Value

data.table of all samples gene expression, whose rows are gene expression and columns are sample names. First column `GENE` contains the corresponding gene names.

### Custom reader function

Custom reader function is given by `read_fun = your_reader_fun`. It takes the filepath as the first argument and return a data.table with the first two columns being `GENE` and `Expression` of type character and double.

The output joint gene expression table has first column `GENE` store the gene name, which are are determined by the first sample being evaluated.

Rest arguments of `create_gene_exp(...)` will be passed to this reader function.

Note: all string-like columns should NOT be of type `factor`. Remember to set `stringsAsFactors = FALSE`.

### Note

The function assumes row order for all samples' gene expressions are the same.

### See Also

`read.table` and `fread` for custom reader function implementation; `create_sample_desc` for creating sample description.

### Examples

    ## Use first three samples of the builtin dataset

    sample_root <- system.file("extdata", package = "iGC")
    sample_desc_pth <- file.path(sample_root, "sample_desc.csv")
    sample_desc <- create_sample_desc(
        sample_desc_pth, sample_root=sample_root
    )[1:3]

    ## Define custom reader function for TCGA level 3 data
    my_gene_exp_reader <- function(ge_filepath) {
        gene_exp <- read.table(
            ge_filepath,
            header = FALSE, skip = 2,
            na.strings = "null",
            colClasses = c("character", "double")
        )
        dt <- data.table::as.data.table(gene_exp)
        data.table::setnames(dt, c("GENE", "Expression"))
    }
    gene_exp <- create_gene_exp(
        sample_desc,
        read_fun = my_gene_exp_reader,
        progress_width = 60
    )
    gene_exp[1:5]

[Package iGC version 1.12.0 Index]