tpp2dCreateReport: Create Report of 2D-TPP analysis

Description Usage Arguments Value

View source: R/tpp2dCreateReport.R

Description

Creates a markdown pdf file that summarizes the 2D-TPP analysis by reporting e.g. R version and package versions used

Usage

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tpp2dCreateReport(data = NULL, configFile = NULL, resultPath = NULL,
  documentType = "html_document", configTable = NULL, normalize = TRUE,
  methods = c(""), idVar = "gene_name", fcStr = "rel_fc_",
  fcStrUpdated = "norm_rel_fc_", intensityStr = "signal_sum_",
  addCol = NULL, fcTolerance = NA, r2Cutoff = NA, fcCutoff = NA,
  slopeBounds = c(NA, NA), fTest = FALSE, trRef = "none")

Arguments

data

output data frame from an 2D-TPP analysis

configFile

character string containing a valid system path to a file which summarizes the experimental details of the 2D-TPP experiment or respective data frame

resultPath

character string containing a system path to where the report should be written

documentType

character string indicating which document type the report should have default: "html_document", alternatives: "pdf_document"

configTable

data frame summarizing the experimental details of the 2D-TPP experiment

normalize

boolean flag indicating whether median normalization has been performed

methods

vector of characters which indicate which methods have been used

idVar

unique protein identifier prefix

fcStr

fold change identifier prefix

fcStrUpdated

character string matching the fold change columns after normalization has been performed

intensityStr

intensity values prefix

addCol

vector of strings indicating which additional data columns were imported

fcTolerance

tolerance for the fcCutoff parameter

r2Cutoff

Quality criterion on dose response curve fit.

fcCutoff

Cutoff for highest compound concentration fold change

slopeBounds

Bounds on the slope parameter for dose response curve fitting

fTest

boolean variable stating whether an fTest was performed

trRef

character string containing a valid system path to a previously generated TPP-TR reference object

Value

A pdf or html report which summarizes all parameters that were set


Bioconductor-mirror/TPP documentation built on July 7, 2017, 11:01 p.m.