pmfanova: pmfanova

In cbroeckl/csu.pmf.tools: a collection of features used internally at CSU PMF for non-targeted metabolomics data processing

pmfanova

Description

perform principle compponent analysis on ramclustR object dataset, export plots

Usage

pmfanova(
  ramclustObj = RC,
  anova.name = NULL,
  which.data = "SpecAbund",
  label.by = "cmpd",
  subset = c(""),
  anova.call = NULL,
  posthoc = NULL,
  effectsplots = TRUE,
  delim = "-",
  plots = TRUE,
  pcut = 0.05,
  p.adj = "BH",
  which.quan = NULL,
  filter = TRUE,
  summary.statistics = TRUE,
  output.summary = TRUE
)

Arguments

ramclustObj	ramclustR object to perform ANOVA on
anova.name	character; optionally assign a name to the anova. valuable if you wish to perform more than one ANOVA on a sample set. If NULL, name will be autogenerated from the anova.call and subset information.
which.data	character; which dataset (SpecAbund or SpecAbundAve) to perform PCA on.
label.by	how should metabolites columns be labelled? one of 'ann' or 'cmpd', typically.
subset	character or integer vector; if character, must be even length. If you wish to perform ANOVA only when your factor called 'treatment' is a 'trt' sample and when 'time' is '3', then you would use i.e. c("treatment", "trt", "time", "3"). vector length must always be even, and with 'factor' followed by 'level'. If an integer vector is provided, only row numbers matching those integers are retained.
anova.call	character; the model you wish to run. i.e. "Trt * Time" or "Trt * Time + (1|Block)"
posthoc	character; if you wish to perform post hoc testing, define the posthoc test to use. i.e. if anova.call is "Trt * Time" you can use "Trt|Time" to specific 'treatment within time' comparisons.
effectsplots	logical; if TRUE, plot effect plots in pdf format. If plotting fails, can set to 'FALSE' to get tabular results only.
delim	character; what is the character delimiting factors in the sample names. generally '-'
plots	logical; if plotting is any issue set this to FALSE.
pcut	numeric; what is the pvalue cutoff for determining significance? Used only for plotting.
p.adj	character; what p.adjust method should be used. generally 'fdr' or 'bh' (equivalent). see ?p.adjust
filter	logical, TRUE by default. when $cmpd.use slot is present (from rc.cmpd.filter.cv function), only cmpds that passed cv filtering are used. If you wish to change that behavior, rerun the rc.cmpd.filter.cv function with a really high CV threshold.
summary.statistics	logical, TRUE by default. If true, calculate mean and standard deviation for each level as defined by the anova.call model.
output.summary	logical, TRUE by default. If true, saves full model results for all ANOVA as .Rdata file, and exports all summaries to a .txt file.
which.quan;	chracter vector. which factors should be interpreted as quantitative? i.e. c("time", "dose")

Details

This function performs standard or mixed model anova using a ramclusR object as input

Value

returns a ramclustR object. new R object in $pca slot. Optionally, new R object in $AuerGervini slot if npc = "auto".

Author(s)

Corey Broeckling

cbroeckl/csu.pmf.tools documentation built on Sept. 30, 2022, 5:40 p.m.