do_batch: Actually runs the batch method, this more than anything shows...

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Actually runs the batch method, this more than anything shows that hpgl_norm is too complicated.

Description

Actually runs the batch method, this more than anything shows that hpgl_norm is too complicated.

Usage

do_batch(
  count_table,
  method = "raw",
  expt_design = expt_design,
  current_state = current_state,
  adjust_method = adjust_method,
  batch_step = 4,
  ...
)

Arguments

count_table	The counts in their current state.
method	Batch/SV method to employ.
expt_design	Experimental design, requiring columns named 'condition' and 'batch'.
current_state	State of the data before messing with it.
adjust_method	Method to use to modify the counts after finding the surrogates.
batch_step	Choose when to perform this in the set of normalization tasks.
...	Extra arguments passed to sva and friends.

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.