constructFeatureTable: constructFeatureTable

View source: R/Functions_class_featureTable.R

constructFeatureTableR Documentation

constructFeatureTable

Description

Constructor function for "MseekFT" object from a feature table data.frame. uses and retains the original data frame plus names of columns containing relevant data.

Usage

constructFeatureTable(
  df = data.frame(mz = numeric(3), rt = numeric(3)),
  mzcol = "mz",
  rtcol = "rt",
  commentcol = "comments",
  fragmentcol = "fragments",
  rtFormat = "sec",
  anagrouptable = NULL,
  tablename = "Custom Table",
  editable = T,
  processHistory = list()
)

Arguments

df

feature table as data.frame, with retention time (rt), mz and (optionally) intensity values.

mzcol

column in df with mz values (columnname), defaults to "mz"

rtcol

column in df with rt values (columnname), defaults to "rt"

commentcol

column in df with comments (columnname), defaults to "comments"

fragmentcol

column in df with fragmentation information (columnname), defaults to "fragments"

rtFormat

Are retention times given in seconds ("sec") or minutes ("min")

anagrouptable

Analysis grouping table: a data.frame with columns "Column" (containing column names from df with intensity values) and "Group" (defining a group for each entry in "Column")

tablename

Name of the table as displayed by Mseek

editable

allow editing of this table in the Mseek app? if FALSE, only comments column can be edited. editable tables are also not paginated.

processHistory

a list of processHistory objects

Details

NOTE: currently, only the default values for column names are supported.

Value

an MseekFT object containing a feature table and metadata


mjhelf/METABOseek documentation built on April 27, 2022, 5:13 p.m.