extract_gct: Exract elements from a GCT matrix
In cmap/cmapR: CMap Tools in R

Description Usage Arguments Value Examples

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.

extract.gct(...)

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

`...`	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`

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

# 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)