Files in iCNV

Integrated Copy Number Variation detection

README.md

NAMESPACE

DESCRIPTION

build/vignette.rds

data/icnv.demo.plrObj_22.rda

data/icnv.demo.array_lrrbaf_22.rda

data/icnv_res0.rda

data/icnv.demo.plrObj_22_2.rda

data/icnv.demo.bambaf_22.rda

R/output_list_function.R R/plot_intensity.R R/plotHMMscore_function.R R/plotindi_function.R R/bed_generator.R R/iCNV_detection_function.R R/icnv_output_to_gb.R R/get_array_input.R R/bambaf_from_vcf.R vignettes/iCNV-vignette.Rmd man/output_list.Rd man/plotHMMscore.Rd man/ngs_plr.pos.Rd man/qcObj.Rd man/chr.Rd man/ngs_baf.pos.Rd man/plotindi.Rd man/icnv_output_to_gb.Rd man/icnv_res0.Rd man/ngs_baf.chr.Rd man/ngs_baf.nm.Rd man/normObj.Rd man/filenm.Rd man/ngs_baf.id.Rd man/ngs_plr.Rd man/iCNV_detection.Rd man/snp_baf.pos.Rd man/get_array_input.Rd man/plot_intensity.Rd man/snp_baf.Rd man/sampname.Rd man/bambaf_from_vcf.Rd man/bed_generator.Rd man/ngs_baf.Rd man/projname.Rd man/snp_lrr.Rd man/sampname_qc.Rd man/snp_lrr.pos.Rd

inst/NEWS

inst/doc/iCNV-vignette.Rmd

inst/doc/iCNV-vignette.html

inst/doc/iCNV-vignette.R

inst/extdata/NA18974.csv.arrayicnv

inst/extdata/NA19152.mapped.ILLUMINA.bwa.YRI.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA19144.csv.arrayicnv

inst/extdata/NA06994.csv.arrayicnv

inst/extdata/NA19204.csv.arrayicnv

inst/extdata/NA18974.mapped.ILLUMINA.bwa.JPT.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA12751.csv.arrayicnv

inst/extdata/NA19098.csv.arrayicnv

inst/extdata/NA19131.mapped.ILLUMINA.bwa.YRI.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA19143.csv.arrayicnv

inst/extdata/NA18969.mapped.ILLUMINA.bwa.JPT.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA19141.csv.arrayicnv

inst/extdata/NA18990.mapped.ILLUMINA.bwa.JPT.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA19160.mapped.ILLUMINA.bwa.YRI.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA18981.mapped.ILLUMINA.bwa.JPT.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA18966.csv.arrayicnv

inst/extdata/NA18970.mapped.ILLUMINA.bwa.JPT.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA18991.csv.arrayicnv

inst/extdata/NA19098.mapped.ILLUMINA.bwa.YRI.exome.20121211.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA19153.mapped.ILLUMINA.bwa.YRI.exome.20121211.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA19119.mapped.ILLUMINA.bwa.YRI.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA18972.csv.arrayicnv

inst/extdata/NA12750.csv.arrayicnv

inst/extdata/NA18971.mapped.ILLUMINA.bwa.JPT.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA10847.mapped.ILLUMINA.bwa.CEU.exome.20121211.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA18971.csv.arrayicnv

inst/extdata/NA19207.csv.arrayicnv

inst/extdata/NA19209.mapped.ILLUMINA.bwa.YRI.exome.20121211.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA11840.mapped.ILLUMINA.bwa.CEU.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA18976.mapped.ILLUMINA.bwa.JPT.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA18975.csv.arrayicnv

inst/extdata/NA19119.csv.arrayicnv

inst/extdata/NA12763.mapped.ILLUMINA.bwa.CEU.exome.20121211.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA19201.mapped.ILLUMINA.bwa.YRI.exome.20121211.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA18991.mapped.ILLUMINA.bwa.JPT.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA12249.mapped.ILLUMINA.bwa.CEU.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA19143.mapped.ILLUMINA.bwa.YRI.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA19171.csv.arrayicnv

inst/extdata/NA19200.mapped.ILLUMINA.bwa.YRI.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA12760.csv.arrayicnv

inst/extdata/NA18973.csv.arrayicnv

inst/extdata/NA19209.csv.arrayicnv

inst/extdata/NA19131.csv.arrayicnv

inst/extdata/NA12760.mapped.ILLUMINA.bwa.CEU.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA19138.csv.arrayicnv

inst/extdata/NA12716.mapped.ILLUMINA.bwa.CEU.exome.20121211.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA18968.csv.arrayicnv

inst/extdata/NA19159.mapped.ILLUMINA.bwa.YRI.exome.20121211.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA19223.csv.arrayicnv

inst/extdata/NA12763.csv.arrayicnv

inst/extdata/NA19210.mapped.ILLUMINA.bwa.YRI.exome.20121211.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA19153.csv.arrayicnv

inst/extdata/NA10847.csv.arrayicnv

inst/extdata/NA18969.csv.arrayicnv

inst/extdata/NA19152.csv.arrayicnv

inst/extdata/NA19141.mapped.ILLUMINA.bwa.YRI.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA18976.csv.arrayicnv

inst/extdata/NA12761.csv.arrayicnv

inst/extdata/NA19223.mapped.ILLUMINA.bwa.YRI.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA18968.mapped.ILLUMINA.bwa.JPT.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA18987.mapped.ILLUMINA.bwa.JPT.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA18973.mapped.ILLUMINA.bwa.JPT.exome.20121211.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA12751.mapped.ILLUMINA.bwa.CEU.exome.20121211.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA19206.csv.arrayicnv

inst/extdata/NA18987.csv.arrayicnv

inst/extdata/NA18981.csv.arrayicnv

inst/extdata/NA19171.mapped.ILLUMINA.bwa.YRI.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA19210.csv.arrayicnv

inst/extdata/NA18967.mapped.ILLUMINA.bwa.JPT.exome.20121211.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA11840.csv.arrayicnv

inst/extdata/NA19159.csv.arrayicnv

inst/extdata/NA19201.csv.arrayicnv

inst/extdata/NA18970.csv.arrayicnv

inst/extdata/NA18975.mapped.ILLUMINA.bwa.JPT.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA12249.csv.arrayicnv

inst/extdata/NA18967.csv.arrayicnv

inst/extdata/NA19144.mapped.ILLUMINA.bwa.YRI.exome.20121211.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA18990.csv.arrayicnv

inst/extdata/NA19137.csv.arrayicnv

inst/extdata/NA19137.mapped.ILLUMINA.bwa.YRI.exome.20130415.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA12716.csv.arrayicnv

inst/extdata/NA19206.mapped.ILLUMINA.bwa.YRI.exome.20121211.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA19160.csv.arrayicnv

inst/extdata/NA19204.mapped.ILLUMINA.bwa.YRI.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA18966.mapped.ILLUMINA.bwa.JPT.exome.20121211.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA19138.mapped.ILLUMINA.bwa.YRI.exome.20121211.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA19200.csv.arrayicnv

inst/extdata/NA19207.mapped.ILLUMINA.bwa.YRI.exome.20121211.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/bam_vcf.list

inst/extdata/NA06994.mapped.ILLUMINA.bwa.CEU.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA12750.mapped.ILLUMINA.bwa.CEU.exome.20130415.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA12761.mapped.ILLUMINA.bwa.CEU.exome.20121211.bam.chr22.sorted.bam.vcf.gz.filter

inst/extdata/NA18972.mapped.ILLUMINA.bwa.JPT.exome.20121211.bam.chr22.sorted.bam.vcf.gz.filter

iCNV documentation built on Nov. 8, 2020, 11:12 p.m.