normalize_se: Normalize a SummarizedExperiment and think about how I want...

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

Normalize a SummarizedExperiment and think about how I want to reimplement some of this.

Description

Normalize a SummarizedExperiment and think about how I want to reimplement some of this.

Usage

normalize_se(
  se,
  transform = "raw",
  norm = "raw",
  convert = "raw",
  batch = "raw",
  filter = FALSE,
  annotations = NULL,
  fasta = NULL,
  entry_type = "gene",
  use_original = FALSE,
  batch1 = "batch",
  batch2 = NULL,
  batch_step = 4,
  low_to_zero = TRUE,
  thresh = 2,
  min_samples = 2,
  p = 0.01,
  A = 1,
  k = 1,
  cv_min = 0.01,
  cv_max = 1000,
  na_to_zero = FALSE,
  adjust_method = "ruv",
  verbose = TRUE,
  ...
)

Arguments

se	Summarized Experiment as input.
transform	Transformation desired, usually log2.
norm	How to normalize the data? (raw, quant, sf, upperquartile, tmm, rle)
convert	Conversion to perform? (raw, cpm, rpkm, cp_seq_m)
batch	Batch effect removal tool to use? (limma sva fsva ruv etc)
filter	Filter out low/undesired features? (cbcb, pofa, kofa, others?)
annotations	Used for rpkm – probably not needed as this is in fData now.
fasta	Fasta file for cp_seq_m counting of oligos.
entry_type	For getting genelengths by feature type (rpkm or cp_seq_m).
use_original	Use the backup data in the expt class?
batch1	Experimental factor to extract first.
batch2	Second factor to remove (only with limma's removebatcheffect()).
batch_step	From step 1-5, when should batch correction be applied?
low_to_zero	When log transforming, change low numbers (< 0) to 0 to avoid NaN?
thresh	Used by cbcb_lowfilter().
min_samples	Also used by cbcb_lowfilter().
p	Used by genefilter's pofa().
A	Also used by genefilter's pofa().
k	Used by genefilter's kofa().
cv_min	Used by genefilter's cv().
cv_max	Also used by genefilter's cv().
na_to_zero	Sometimes rpkm gives some NA values for very low numbers.
adjust_method	Given a set of sv estimates, change the counts with this method.
verbose	Print what is happening while the normalization is performed? I am not sure why, but I think they should be 0.
...	more options

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