Simple Peak Alignment for Gas-Chromatography Data
GCalignR: A Package to Align Gas Chromatography Peaks Based on Retenti...
Full Alignment of Peak Lists by linear retention time correction.
Aligning peaks based on retention times
align peaks individually among chromatograms
align peaks individually among chromatograms
Output aligned data in form of a data frame for each variable
Subtraction of blank readings from sample readings
Check input prior to processing in GCalignR
Select the optimal reference for full alignments of peak lists
Visualise peak lists as a pseudo-chromatogram
Detect local maxima in time series
Visualises peak alignments in form of a heatmap
Merge redundant rows
Normalisation of peak abundancies
Estimate the observed space between peaks within chromatograms
Plot diagnostics for an GCalign Object
Summarising Peak Alignments with GCalignR
Import data from single EMPOWER2 HPLC files
Read content of a text file and convert it to a list
Remove peaks present in negative control samples
Remove singletons
Simulate simple chromatograms
Aligns peak based on peak retention times and matches homologous peaks across samples. The underlying alignment procedure comprises three sequential steps. (1) Full alignment of samples by linear transformation of retention times to maximise similarity among homologous peaks (2) Partial alignment of peaks within a user-defined retention time window to cluster homologous peaks (3) Merging rows that are likely representing homologous substances (i.e. no sample shows peaks in both rows and the rows have similar retention time means). The algorithm is described in detail in Ottensmann et al., 2018 <doi:10.1371/journal.pone.0198311>.