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.
1 2 3 4 5 6 7 8 9 10 11 | 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
1 2 3 4 5 6 | # 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)
|
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