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| align | Align peaks for a specified precision. |
| avesd | Compute the Average Standard Deviation for a Set of Spectra and a Given Cutoff Point |
| aveSpec | Compute mean spectrum of a set of spectra |
| binning | Binning the Mass Spectrometry Data |
| bslnoff | Baseline Substraction |
| gelmap | Plot the image of a set of spectra |
| getMzs | Extract M/Z values from the biomarker dataframe. |
| getPeaks | Peak Detection |
| getPeaks2 | Quantify peaks for individual spectra. |
| intg | Integration |
| is.multiple | Find multiple-charged polypeptides. |
| isPeak | Locate Peaks in a Spectrum |
| lnn | Estimate Signal and Variation of a Spectrum |
| noise | Peak Detection |
| peaks | Peak Detection |
| pk2bmkr | Find Biomarkers. |
| quality | Quality Check on a Set of Spectra |
| read.files | Read a Spectrum from a Comma Deliminated File |
| renorm | Renormalize Spectra |
| rmBaseline | Batch Baseline Subtraction. |
| sigma | Peak Detection |
| specZoom | Plotting a Spectrum with Peaks |