create_ramclustObj {RAMClustR}

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.