RAMClustR (version 1.3.1)

create_ramclustObj: 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
)

Value

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

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.