correcting: correcting

In SciDoPhenIA/phenomis: Analysis of single and multiple phenomic data sets

correcting

Description

Signal drift and batch effect correction

Usage

correcting(
  x,
  method.vc = c("loess", "serrf")[1],
  reference.vc = c("pool", "sample")[1],
  loess_span.vn = 1,
  serrf_corvar.vi = 10,
  sample_intensity.c = c("median", "mean", "sum")[2],
  title.c = NA,
  col_batch.c = "batch",
  col_injectionOrder.c = "injectionOrder",
  col_sampleType.c = "sampleType",
  figure.c = c("none", "interactive", "myfile.pdf")[2],
  report.c = c("none", "interactive", "myfile.txt")[2]
)

## S4 method for signature 'MultiAssayExperiment'
correcting(
  x,
  method.vc = c("loess", "serrf")[1],
  reference.vc = c("pool", "sample")[1],
  loess_span.vn = 1,
  serrf_corvar.vi = 10,
  sample_intensity.c = c("median", "mean", "sum")[2],
  title.c = NA,
  col_batch.c = "batch",
  col_injectionOrder.c = "injectionOrder",
  col_sampleType.c = "sampleType",
  figure.c = c("none", "interactive", "myfile.pdf")[2],
  report.c = c("none", "interactive", "myfile.txt")[2]
)

## S4 method for signature 'SummarizedExperiment'
correcting(
  x,
  method.vc = c("loess", "serrf")[1],
  reference.vc = c("pool", "sample")[1],
  loess_span.vn = 1,
  serrf_corvar.vi = 10,
  sample_intensity.c = c("median", "mean", "sum")[2],
  title.c = NA,
  col_batch.c = "batch",
  col_injectionOrder.c = "injectionOrder",
  col_sampleType.c = "sampleType",
  figure.c = c("none", "interactive", "myfile.pdf")[2],
  report.c = c("none", "interactive", "myfile.txt")[2]
)

## S4 method for signature 'MultiDataSet'
correcting(
  x,
  method.vc = c("loess", "serrf")[1],
  reference.vc = c("pool", "sample")[1],
  loess_span.vn = 1,
  serrf_corvar.vi = 10,
  sample_intensity.c = c("median", "mean", "sum")[2],
  title.c = NA,
  col_batch.c = "batch",
  col_injectionOrder.c = "injectionOrder",
  col_sampleType.c = "sampleType",
  figure.c = c("none", "interactive", "myfile.pdf")[2],
  report.c = c("none", "interactive", "myfile.txt")[2]
)

## S4 method for signature 'ExpressionSet'
correcting(
  x,
  method.vc = c("loess", "serrf")[1],
  reference.vc = c("pool", "sample")[1],
  loess_span.vn = 1,
  serrf_corvar.vi = 10,
  sample_intensity.c = c("median", "mean", "sum")[2],
  title.c = NA,
  col_batch.c = "batch",
  col_injectionOrder.c = "injectionOrder",
  col_sampleType.c = "sampleType",
  figure.c = c("none", "interactive", "myfile.pdf")[2],
  report.c = c("none", "interactive", "myfile.txt")[2]
)

Arguments

x	An S4 object of class SummarizedExperiment or MultiAssayExperiment
method.vc	character of length 1 or the total number of datasets: method(s) to be used for each dataset (either 'serrf' or 'loess'); in case the parameter is of length 1 and x contains multiple datasets, the same method will be used for all datasets
reference.vc	character of length 1 or the total number of datasets: sample type to be used as reference for the correction (as indicated in the 'sampleType' column from the colData(x); e.g. 'pool' [default]); should be set to 'pool' for the 'serrf' method; in case the parameter is of length 1 and x contains multiple datasets, the same reference sample type will be used for all datasets
loess_span.vn	character of length 1 or the total number of datasets: smoothing parameter for the loess regression; between 0 and 1; (default set to 1); in case the parameter is of length 1 and x contains multiple datasets, the same span value will be used for all datasets
serrf_corvar.vi	character of length 1 or the total number of datasets: number of correlated features for the random forest regression; (default set to 10); in case the parameter is of length 1 and x contains multiple datasets, the same value will be used for all datasets
sample_intensity.c	Character: metric to be used when displaying the sample intensities
title.c	Character: Graphic title: if NA [default] the 'title' slot from the experimentData will be used (metadata)
col_batch.c	Character: name of the column from colData(x) containing the batch information (encoded as characters)
col_injectionOrder.c	Character: name of the column from colData(x) containing the injection order information (encoded as numerics)
col_sampleType.c	Character: name of the column from colData(x) containing the sample type information (encoded as characters)
figure.c	Character: File name with '.pdf' extension for the figure; if 'interactive' (default), figures will be displayed interactively; if 'none', no figure will be generated
report.c	Character: File name with '.txt' extension for the printed results (call to sink()'); if 'interactive' (default), messages will be printed on the screen; if 'none', no verbose will be generated

Value

SummarizedExperiment or MultiAssayExperiment including the corrected intensities in the assay matrix (matrices)

Examples

sacurine.se <- reading(system.file("extdata/W4M00001_Sacurine-statistics", package = "phenomis"))
sacurine.se <- correcting(sacurine.se)
# MultiDataSet (to be done)

SciDoPhenIA/phenomis documentation built on June 9, 2022, 11:54 p.m.