create_ramclustObj: create_ramclustObj

In RAMClustR: Mass Spectrometry Metabolomics Feature Clustering and Interpretation

create_ramclustObj

Description

create ramclustr Object

Usage

create_ramclustObj(
  ExpDes = NULL,
  input_history = NULL,
  MSdata = NULL,
  MSMSdata = NULL,
  frt = NULL,
  fmz = NULL,
  st = NULL,
  phenoData = NULL,
  feature_names = NULL,
  sample_names = NULL,
  xcmsOrd = NULL,
  ensure.no.na = TRUE
)

Arguments

ExpDes	either an R object created by R ExpDes object: data used for record keeping and labelling msp spectral output
input_history	input history
MSdata	dataframe containing MS Data
MSMSdata	dataframe containing MSMS Data
frt	feature retention time, in whatever units were fed in
fmz	feature retention time
st	numeric: sigma t - time similarity decay value
phenoData	dataframe containing phenoData
feature_names	feature names extracted from the data
sample_names	sample names extracted from the data
xcmsOrd	original xcms order of features, for back-referencing when necessary
ensure.no.na	logical: if TRUE, any 'NA' values in msint and/or msmsint are replaced with numerical values based on 10 percent of feature min plus noise. Used to ensure that spectra are not written with NA values.

Value

an ramclustR object. this object is formatted as an hclust object with additional slots for holding feature and compound data.

RAMClustR documentation built on Oct. 20, 2023, 5:08 p.m.