getChromatogramDataPoints_: Extract Chromatographic data (Retention Time and Intensity)...
In singjc/mstools: OpenSWATH Mass Spectrometry Data Exploration

Description Usage Arguments Value Author(s)

View source: R/getChromatogramDataPoints.R

This function can be used to extract chromatogram retention and intensity values for a given list of fragment ids.

getChromatogramDataPoints_(
  filename,
  frag_ids,
  id_type = "transition_ids",
  name_time = "RT",
  name_intensity = "Int",
  mzPntrs = NULL,
  SgolayFiltOrd = NULL,
  SgolayFiltLen = NULL
)

`filename`	A character vector of the absolute path and filename of the chromatogram file. (Must be .mzML or sqMass format)
`frag_ids`	A list of a vector containing fragment ids
`id_type`	A character indicating if the passed frag_ids is of type 'transition_ids' or 'chromatogramIndex'
`name_time`	A character vector to name retention column
`name_intensity`	A character vector to name Intensity column. You can pass a character vectory of a function that will be evaluated to a string. i.e. "paste0('X', data_row$FRAGMENT_ID )"
`mzPntrs`	A list object containing cached mzR objects.
`SgolayFiltOrd`	(integer) It defines the polynomial order of filer.
`SgolayFiltLen`	(integer) Must be an odd number. It defines the length of filter.