counts_from_surrogates: A single place to extract count tables from a set of...

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

A single place to extract count tables from a set of surrogate variables.

Description

Given an initial set of counts and a series of surrogates, what would the resulting count table look like? Hopefully this function answers that question.

Usage

counts_from_surrogates(
  data,
  adjust = NULL,
  design = NULL,
  method = "ruv",
  cond_column = "condition",
  batch_column = "batch",
  matrix_scale = "linear",
  return_scale = "linear",
  ...
)

Arguments

data	Original count table, may be an expt/expressionset or df/matrix.
adjust	Surrogates with which to adjust the data.
design	Experimental design if it is not included in the expressionset.
method	Which methodology to follow, ideally these agree but that seems untrue.
cond_column	design column containing the condition data.
batch_column	design column with the batch data, used for subtractive methods.
matrix_scale	Was the input for the surrogate estimator on a log or linear scale?
return_scale	Does one want the output linear or log?
...	Arguments passed to downstream functions.

Value

A data frame of adjusted counts.

See Also

[sva] [RUVSeq] [crossprod()] [tcrossprod()] [solve()]

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