Nothing
## ---- echo = FALSE------------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.width=9,
fig.height=6
)
## ----runApp, eval=FALSE-------------------------------------------------------
# umiAnalyzer::runUmiVisualizer()
## ----example1, eval=TRUE------------------------------------------------------
library(umiAnalyzer)
main <- system.file("extdata", package = "umiAnalyzer")
simsen <- createUmiExperiment(main)
simsen <- mergeAssays(
object = simsen,
name = "new",
assay.list = c("PIK3CA_123", "PIK3CA_234")
)
## ----bam-files, eval=TRUE-----------------------------------------------------
reads <- parseBamFiles(main, consDepth = 10)
BarcodeFamilyHistogram(reads)
## ----example1continued, eval=TRUE---------------------------------------------
QCplot(simsen)
## ----filerobject, eval=TRUE---------------------------------------------------
simsen <- filterUmiObject(simsen)
## ----example1continued_2, eval=TRUE-------------------------------------------
# This is optional
simsen <- callVariants(simsen)
## ----getFilter, eval=TRUE-----------------------------------------------------
myfilter <- getFilteredData(simsen)
myfilter
## ----example1continued_3, eval=TRUE-------------------------------------------
UmiCountsPlot(simsen)
## ---- eval=FALSE--------------------------------------------------------------
# AmpliconPlot(simsen)
## ---- eval=FALSE--------------------------------------------------------------
# AmpliconPlot(
# object = simsen,
# amplicons = 'KIT_125',
# samples = 'VAF-1-5ng-1-10x'
# )
## ----metaDataImport, eval=FALSE-----------------------------------------------
# metaData <- system.file("extdata", "metadata.txt", package = "umiAnalyzer")
#
# simsen <- importDesign(
# object = simsen,
# file = metaData
# )
#
# design <- getMetaData(
# object = simsen,
# attributeName = "design"
# )
#
# design
## ----time_course, eval=FALSE--------------------------------------------------
# simsen <- umiAnalyzer::analyzeTimeSeries(
# object = simsen,
# time.var = 'time',
# group.by = 'replicate'
# )
## ----replicates, eval=FALSE---------------------------------------------------
# simsen <- mergeTechnicalReplicates(
# object = simsen,
# group.by = 'replicate',
# option = 'Set1',
# amplicons = c('new', 'TP53_1', 'TP53_7')
# )
## ----vizMerge, eval=FALSE-----------------------------------------------------
# vizMergedData(
# simsen,
# amplicons = c('new')
# )
## ----example2, eval=FALSE-----------------------------------------------------
# simsen <- callVariants(simsen)
#
# simsen <- filterVariants(simsen)
#
# simsen <- generateAmpliconPlots(
# object = simsen
# )
## ----vcf, eval=FALSE----------------------------------------------------------
# generateVCF(object = simsen, outFile = 'simsen.vcf', printAll = FALSE, save = FALSE)
## ----csv, eval=FALSE----------------------------------------------------------
# consensus_data <- saveConsData(object = simsen)
#
# outDir <- getwd()
# saveConsData(object = simsen, outDir = outDir, delim = ';', save = TRUE)
## ----sessionInfo--------------------------------------------------------------
sessionInfo()
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