extract.gct {cmapR} | R Documentation |
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 |
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 |
cdesc |
a |
row_keyfield |
the column name of |
col_keyfield |
the column name of |
a list of the following elements
a logical matrix of the same dimensions as
ds@mat
indicating which matrix elements have
been extracted
an array index into ds@mat
representing which elements have been extracted
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)