inspecting: Inspecting

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

Inspecting

Description

Provides numerical metrics and graphical overview of an ExpressionSet or MultiDataSet instance Please note that all variables with a proportion of missing values > 'max_na_prop.n' or a variance of 0 will be filtered out at the beginning of the method and therefore in the output SummarizedExperiments(s)

Usage

inspecting(
  x,
  pool_as_pool1.l = FALSE,
  pool_cv.n = 0.3,
  loess_span.n = 1,
  sample_intensity.c = c("median", "mean", "sum")[2],
  title.c = NA,
  plot_dims.l = TRUE,
  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'
inspecting(
  x,
  pool_as_pool1.l = FALSE,
  pool_cv.n = 0.3,
  loess_span.n = 1,
  sample_intensity.c = c("median", "mean", "sum")[2],
  title.c = NA,
  plot_dims.l = TRUE,
  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'
inspecting(
  x,
  pool_as_pool1.l = FALSE,
  pool_cv.n = 0.3,
  loess_span.n = 1,
  sample_intensity.c = c("median", "mean", "sum")[2],
  title.c = NA,
  plot_dims.l = TRUE,
  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'
inspecting(
  x,
  pool_as_pool1.l = FALSE,
  pool_cv.n = 0.3,
  loess_span.n = 1,
  sample_intensity.c = c("median", "mean", "sum")[2],
  title.c = NA,
  plot_dims.l = TRUE,
  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'
inspecting(
  x,
  pool_as_pool1.l = FALSE,
  pool_cv.n = 0.3,
  loess_span.n = 1,
  sample_intensity.c = c("median", "mean", "sum")[2],
  title.c = NA,
  plot_dims.l = TRUE,
  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
pool_as_pool1.l	Logical: should pool be included (as pool1) in the correlation with the dilution factor?
pool_cv.n	Numeric: threshold for the coefficient of variation of the pools
loess_span.n	Numeric: span parameter used in the loess trend estimation
sample_intensity.c	Character: function to be used to display the global sample intensity; default: 'mean'
title.c	Character: MultiAssayExperiment: title of the barplot showing the number of samples and variables in each dataset; ExpressionSet: title of the multipanel graphic displaying the metrics (if NA -default- the title slot from the experimentData will be used)
plot_dims.l	(MultiAssayExperiment) Logical: should an overview of the number of samples and variables in all datasets be barplotted?
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 computed in rowData and colData sample and variable metrics

Examples

sacurine.se <- reading(system.file("extdata/W4M00001_Sacurine-statistics", package = "phenomis"))
sacurine.se <- inspecting(sacurine.se)
sacurine.se <- correcting(sacurine.se)
sacurine.se <- inspecting(sacurine.se)
sacurine.se <- transforming(sacurine.se)
sacurine.se <- inspecting(sacurine.se)
# MultiAssayExperiment
prometis.mae <- reading(system.file("extdata/prometis", package = "phenomis"))
## Not run: 
prometis.mae <- inspecting(prometis.mae)

## End(Not run)

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