Description Usage Arguments Value Examples
controls #' Fetch the same plate control samples applicable for given ids (distil_id). Expects that the specified ids have pert_type of trt_sh or trt_cp.
1 2 3 4 |
x |
A slinky object |
ids |
The distil_id(s) to lookup. |
verbose |
Do you want to know how things are going? Default is FALSE. |
cl |
Optional cluster object to parallelize this
operation. If verbose is TRUE, use this pattern in order for
progress bar to update:
|
The name of the vehicle control for the queried perturbagen(s). \For a given set of distil_ids, this function finds the distil_ids for the corresponding control samples based on the the pert_type and (for trt_cp) the specified vehicle. The returned dataframe can be used, among other things, to create a control dataset for differential expression or other analysis. See also diffexp.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | # for build/demo only. You MUST use your own key when using the slinky
# package.
user_key <- httr::content(httr::GET('https://api.clue.io/temp_api_key'),
as='parsed')$user_key
sl <- Slinky(user_key,
system.file('extdata', 'demo.gctx',
package='slinky'),
system.file('extdata', 'demo_inst_info.txt',
package = 'slinky'))
amox_gold <- clueInstances(sl, where_clause = list("pert_type" = "trt_cp",
"pert_iname" = "amoxicillin",
"cell_id" = "MCF7",
"is_gold" = TRUE),
poscon = "omit")
colnames(sl[,1:5])
rownames(sl[1:5,1:5])
ids.ctrl <- controls(sl, ids = amox_gold)$distil_id
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