extract.gct {cmapR} | R Documentation

## Exract elements from a GCT matrix

### Description

extract the elements from a `GCT` object where the values of `row_field` and `col_field` are the same. A concrete example is if `g` represents a matrix of signatures of genetic perturbations, and you wan to extract all the values of the targeted genes.

### Usage

    extract.gct(...)

    extract_gct(
      g,
      row_field,
      col_field,
      rdesc = NULL,
      cdesc = NULL,
      row_keyfield = "id",
      col_keyfield = "id"
    )

### Arguments

`...` | arguments passed on to `extract_gct`
`g` | the GCT object
`row_field` | the column name in rdesc to search on
`col_field` | the column name in cdesc to search on
`rdesc` | a `data.frame` of row annotations
`cdesc` | a `data.frame` of column annotations
`row_keyfield` | the column name of `rdesc` to use for annotating the rows of `g`
`col_keyfield` | the column name of `cdesc` to use for annotating the rows of `g`

### Value

a list of the following elements

mask

  a logical matrix of the same dimensions as `ds@mat` indicating which matrix elements have been extracted

idx

  an array index into `ds@mat` representing which elements have been extracted

vals

  a vector of the extracted values

### Examples

    # get the values for all targeted genes from a
    # dataset of knockdown experiments
    res <- extract_gct(kd_gct, row_field="pr_gene_symbol",
      col_field="pert_mfc_desc")
    str(res)
    stats::quantile(res$vals)

[Package cmapR version 1.2.1 Index]