wkumler / RaMS

R-based access to Mass-Spectrometry data
Other
22 stars 7 forks source link

grabMzxmlBPC still uses old method to determine RT unit #28

Closed wkumler closed 7 months ago

wkumler commented 8 months ago
grabMzxmlBPC <- function(xml_data, TIC=FALSE, rtrange, incl_polarity){
  scan_nodes <- xml2::xml_find_all(
    xml_data, '//d1:scan[@msLevel="1"]'
  )
  rt_chrs <- xml2::xml_attr(scan_nodes, "retentionTime")
  rt_vals <- as.numeric(gsub(pattern = "PT|S", replacement = "", rt_chrs))
  if(any(rt_vals>150)){rt_vals <- rt_vals/60}

  int_attr <- ifelse(TIC, "totIonCurrent", "basePeakIntensity")
  int_vals <- as.numeric(xml2::xml_attr(scan_nodes, int_attr))
  if(!is.null(rtrange)){
    int_vals <- int_vals[rt_vals%between%rtrange]
    rt_vals <- rt_vals[rt_vals%between%rtrange]
  }

  return(data.table(rt=rt_vals, int=int_vals))
}

Should instead be the method that was patched in another PR I don't have the brainspace to find right now

wkumler commented 7 months ago

Fixed with #33