options()
(#98, #99)load_dataset
warn about repeated Sample+Replicate+Locus entries
across rows (#90)load_config
warn about any unrecognized configuration file entries
(#88)load_csv
use custom row names if given (#74)save_csv
automatically create any parent directories as needed
(#63)pheatmap
arguments in plot_dist_mat
(#62)load_csv
and save_csv
functions to centralize loading and saving
tabular data (#43).plot_heatmap
for cases with blank
results and only one unique non-blank value (#22).analyze_dataset
for locus name mismatches between dataset
table and locus attributes table (#21).prepare_dataset
for missing data directory (#20).prepare_dataset
for zero-detected-files case.load_dataset
for missing data files.full_analysis
to warn if any input data files are
completely empty.match_known_genotypes
.categorize_genotype_results
.summarize_dataset
when Name column is
supplied in results summary data frame.save_seqfile_data
, to save a directory tree
of per-sequence-file output files starting from the first shared directory
in the input file paths.analyze_sample
into a new analyze_seqs
function to be used as a separate step (enabling shared processing between
multiplexed samples in a single data file for #3).analyze_dataset
output into two separate lists
called files and samples.analyze_dataset
. The summary data frame
now has Allele1Name and Allele2Name columns, and the sample data frames a
SeqName column, matching any sequence recognized as a called allele from any
sample in the current analysis (or a previous analysis if the allele table
is provided).histogram
function to recognize more categories of unique
sequences including sequences called as alleles elsewhere, and return the
counts-by-length data by category in a list.histogram2
to centralize functionality in histogram
.summarize_sample_by_length
function.summarize_sample
functions to allow any combination
of TRUE/FALSE values in the Ambiguous/Stutter/Artifact entries. Previously
only the first (highest-count) case would be flagged.analyze_sample
output to flag sequences
with non-ACTG characters.summarize_sample
output to track
filtering of sequences with non-ACTG characters.Add the following code to your website.
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