subMaldi: Organization and Processing of MALDI-MS Datasets

Description Usage Arguments Value Warning Author(s) References See Also Examples

Fills in the columns of the empty data frame created using createSpecDF. Mass to charge values from pairwise spectral data are compared to the full_mz vector. All peaks within the thresh of one another are binned, and only the maximum intensity of that bin is filled into the mapped spectrum.

mapSpectrum(
  dat,
  massCol,
  intenseCol,
  dig = 4,
  thresh = 1e-04,
  spec_df,
  colName
)

`dat`	A pairwise data frame containing your spectral data. Should contain two columns: one for m/z and one for intensity.
`massCol`	A character string; the name of the m/z column in `dat`.
`intenseCol`	A character string; the name of the intensity column in `dat`.
`dig`	Number of decimal places to round the m/z data to; must match the same value used in `createSpecDF` in order for the columns to fill. Default = 4.
`thresh`	Single numeric value; all m/z values within `thresh` of each other are binned under that with the maximum intensity. Default = 5e-5.
`spec_df`	An empty data frame created using `createSpecDF`.
`colName`	A character string; the name of the column that should be filled with the spectral data.

Returns a vector that is used to fill in the colName column of the mapped spectral data frame.

It is important that the values for thresh and dig are equal to that of res and dig used in createSpecDF(). Otherwise the data will fail to map.

Kristen Yeh <kristenyeh@trentu.ca> Wesley Burr <wesleyburr@trentu.ca>

https://github.com/wesleyburr/subMaldi

createSpecDF

## Load sample dataset "Blank1.rda"
data("lank1")

## Create empty spectral data frame to map to
spec_df <- createSpecDF(min_mz = 53.76, max_mz = 1100, res = 0.0001, dig = 4)

## Map binary spectral data to empty spectral data frame
spec_df <- mapSpectrum(dat = Blank1, massCol = "mass", intenseCol = "Intensity", 
            spec_df = spec_df, colName = "Sample", thresh = 1e-04, dig = 4)