Man pages for bahlolab/exSTRa
Expanded STR algorithm: detecting expansions in Illumina sequencing data

as.exstra_scoreConvert a compatable object to the exstra_score class
copy.exstra_scoreCopy an exstra_score object.
copy.exstra_tsumCopy an exstra_tsum object
dim.exstra_scoreDimension of exstra_score object
exSTRaExpanded STR algorithm
exstra_knownKnown repeat expansion disorder loci.
exstra_tsum_new_Create a new exstra_tsum object.
exstra_wgs_pcr_2Repeat score data from cohort WGS_PCR_2.
is.exstra_scoreTest if object is an exstra_score object
is.exstra_tsumCheck if an object is an instance of the exstra_tsum class.
length.exstra_scoreNumber of data points in exstra_score object
lociReturn the loci of the selected object
plot.exstra_scorePlot ECDF curves from an exstra_score object
plot.exstra_tsumPlot exstra_tsum, highlighting significant results
plot_multiMultiple STR score ECDF plots
p_valuesReturn a data.table with p-values of a tsum_exstra object.
p_value_sd_P-value standard deviation
qm_tsum_stat_bare_simple tsum statistic by known
rbind_score_listCombine multiple exSTRa data objects.
read_exstra_dbRead a file of known STR loci for analysis
read_scoreRead repeat score data produced from Bio::STR::exSTRa
sub-.exstra_scoreExtract loci or samples frome exstra_score object
sub-.exstra_tsumExtract loci or samples from exstra_tsum object
suggested_exstra_pipelineCreate a graph of the suggested pipeline
tsum_p_value_summarycreate summary of significance on a exstra_tsum object
tsum_statistic_1locusDetermine tsum_statistic_1locus assuming input data is for...
tsum_testGenerate T sum statistics and p-values from simulation.
tsum_test_1Generate T sum statistics and p-values from simulation.
bahlolab/exSTRa documentation built on Sept. 3, 2018, 2:40 p.m.