gc_peak_df
from align_peaks
choose_optimal_reference
that always selected the first sample as a reference. Thanks to Heberto del Rio who pointed this out on https://github.com/mottensmann/GCalignR/issues/27max_diff_peak2mean = 0
: In this special case there is no need to use a time-consuming iterative approach but peaks can be sorted simply based on absolute values. This is implemented in two steps. (1) Across all samples, unique retention times are extracted, sorted in increasing temporal order and written to a template data frame. (2) For each sample, peaks are matched to the corresponding row of the template data frame.gc_heatmap
.fill = TRUE
as a parameter in utils::read.table
when reading data from text within internal functions. Loading GC data with utils::read.table failed in cases of missing values in a column (i.e. empty). This is the correct behaviour as missing data should always be coded explicitly by ‘NA’remove_empty
for the main function align_chromatograms
. If samples are empty (i.e.. no peak) this parameter allows to remove those cases from the dataset to avoid problems in post-hoc analyses. By default FALSE
, i.e.. all but the blank samples are kept.permute
for the functions align_chromatograms
and align_peaks
. This allows to change the default behaviour of random permutation of samples during the alignment and might be useful if exact replication is needed.read_empower2
allows to import HPLC data that has been generated using the EMPOWER 2 softwareBugfixes
New functions implemented
choose_optimal_reference
offers an automatism to pick suitable references.draw_chromatograms
allows to represent a peak list in form of chromatogram.remove_blanks
allows to get rid of peaks that represent contamination after aligning a datasetremove_singletons
allows to remove single peaks from the dataset after aligningmerge_redundant_rows
allows to merge rows that were not recognised as redundant during the alignment by increasing the threshold value for the evaluation of similarityAlgorithm
pbapply
, we implemented progress bars to inform the user about the progress and the estimated running time of intermediate steps in the alignment of peak lists.warning messages
Plots
plot.GCalign
.gc_heatmap
.draw_chromatograms
was added as another visualisation tool.Vignettes
Documentation