Files in AlineTalhouk/FluidigmValidation
VALIDATE FLUIDIGM MACHINE DATA
.Rbuildignore
.gitignore
DESCRIPTION
FluidigmValidation.Rproj
Mutation for every amplicons.xls
NAMESPACE
R/checkAllFiles.R
R/checkFC.R
R/filterPassDepth.R
R/filterQualityFrequency.R
R/fluidigmValidationMain.R
R/getPatientID.R
R/labelMutationGroup.R
R/labelTumorType.R
R/notMutationGroupException.R
R/onceN.R
R/onceT1.R
R/onceT2.R
R/onlyRepetitivePos.R
R/organize.R
R/passSummary.R
R/processAmpliconInfo.R
R/renameToTxt.R
R/splitINFO.R
R/twiceT1.R
R/twiceT2.R
data/PAT37DNA48OPC3S19.rda
data/PAT82DNA130CurettageA2S9.rda
data/dataForCheckFC.rda
data/dataForFilterQualityFrequency.rda
fluidigmLogicalTable.xlsx
fluidigmValidationMainTestData/PAT-ID100-DNA-ID161-OP-B4_S26.vcf
fluidigmValidationMainTestData/PAT-ID100-DNA-ID161-OP-C4_S27.vcf
fluidigmValidationMainTestData/PAT-ID100-DNA-ID162-NORMAL-D4_S28.vcf
fluidigmValidationMainTestData/PAT-ID101-DNA-ID163-OP-E4_S29.vcf
fluidigmValidationMainTestData/PAT-ID101-DNA-ID163-OP-F4_S30.vcf
fluidigmValidationMainTestData/PAT-ID101-DNA-ID164-NORMAL-G4_S31.vcf
fluidigmValidationMainTestData/PAT-ID63-DNA-ID100-NORMAL-C1_S3.vcf
fluidigmValidationMainTestData/PAT-ID63-DNA-ID99-OP-A1_S1.vcf
fluidigmValidationMainTestData/PAT-ID63-DNA-ID99-OP-B1_S2.vcf
fluidigmValidationMainTestData/PAT-ID64-DNA-ID101-Curettage-D1_S4.vcf
fluidigmValidationMainTestData/PAT-ID64-DNA-ID101-Curettage-E1_S5.vcf
fluidigmValidationMainTestData/PAT-ID64-DNA-ID1132-NORMAL-F1_S6.vcf
fluidigmValidationMainTestData/PAT-ID82-DNA-ID129-OP-G1_S7.vcf
fluidigmValidationMainTestData/PAT-ID82-DNA-ID129-OP-H1_S8.vcf
fluidigmValidationMainTestData/PAT-ID82-DNA-ID130-Curettage-A2_S9.vcf
fluidigmValidationMainTestData/PAT-ID82-DNA-ID130-Curettage-B2_S10.vcf
fluidigmValidationMainTestData/PAT-ID82-DNA-ID131-NORMAL-C2_S11.vcf
fluidigmValidationMainTestData/PAT-ID95-DNA-ID149-OP-D2_S12.vcf
fluidigmValidationMainTestData/PAT-ID95-DNA-ID149-OP-E2_S13.vcf
fluidigmValidationMainTestData/PAT-ID95-DNA-ID150-NORMAL-F2_S14.vcf
fluidigmValidationMainTestData/PAT-ID96-DNA-ID151-OP-G2_S15.vcf
fluidigmValidationMainTestData/PAT-ID96-DNA-ID151-OP-H2_S16.vcf
fluidigmValidationMainTestData/PAT-ID96-DNA-ID152-NORMAL-A3_S17.vcf
fluidigmValidationMainTestData/PAT-ID96-DNA-ID152-NORMAL-C3_S19.vcf
fluidigmValidationMainTestData/PAT-ID98-DNA-ID156-OP-B3_S18.vcf
fluidigmValidationMainTestData/PAT-ID98-DNA-ID157-NORMAL-D3_S20.vcf
fluidigmValidationMainTestData/PAT-ID99-DNA-ID158-OP-E3_S21.vcf
fluidigmValidationMainTestData/PAT-ID99-DNA-ID158-OP-F3_S22.vcf
fluidigmValidationMainTestData/PAT-ID99-DNA-ID159-Curettage-G3_S23.vcf
fluidigmValidationMainTestData/PAT-ID99-DNA-ID159-Curettage-H3_S24.vcf
fluidigmValidationMainTestData/PAT-ID99-DNA-ID160-NORMAL-A4_S25.vcf
man/checkAllFiles.Rd
man/checkFC.Rd
man/filterPassDepth.Rd
man/filterQualityFrequency.Rd
man/fluidigmValidationMain.Rd
man/getPatientID.Rd
man/labelMutationGroup.Rd
man/labelTumorType.Rd
man/notMutationGroupException.Rd
man/onceN.Rd
man/onceT1.Rd
man/onceT2.Rd
man/onlyRepetitivePos.Rd
man/organize.Rd
man/passSummary.Rd
man/processAmpliconInfo.Rd
man/renameToTxt.Rd
man/splitINFO.Rd
man/twiceT1.Rd
man/twiceT2.Rd
passSummaryTestData/PAT-ID24-33-OP-D1_S98.genome.vcf
passSummaryTestData/PAT-ID44-65-OP-B2_S104.genome.vcf
testData/A/PAT-ID37-DNA-ID48-OP-C3_S19.vcf
testData/A/PAT-ID37-DNA-ID48-OP-D3_S20.vcf
testData/A/PAT-ID37-DNA-ID49-Curettage-E3_S21.vcf
testData/A/PAT-ID37-DNA-ID49-Curettage-F3_S22.vcf
testData/A/PAT-ID37-DNA-ID50-NORMAL-G3_S23.vcf
testData/A/PAT-ID63-DNA-ID100-NORMAL-C1_S3.vcf
testData/A/PAT-ID63-DNA-ID99-OP-A1_S1.vcf
testData/A/PAT-ID63-DNA-ID99-OP-B1_S2.vcf
testData/A/PAT-ID64-DNA-ID101-Curettage-D1_S4.vcf
testData/A/PAT-ID64-DNA-ID101-Curettage-E1_S5.vcf
testData/A/PAT-ID64-DNA-ID1132-NORMAL-F1_S6.vcf
testData/A/PAT-ID82-DNA-ID129-OP-B1_S140.vcf
testData/A/PAT-ID82-DNA-ID129-OP-G1_S7.vcf
testData/A/PAT-ID82-DNA-ID129-OP-H1_S8.vcf
testData/A/PAT-ID82-DNA-ID130-Curettage-A2_S9.vcf
testData/A/PAT-ID82-DNA-ID130-Curettage-B2_S10.vcf
testData/A/PAT-ID82-DNA-ID130-Curettage-C1_S141.vcf
testData/A/PAT-ID82-DNA-ID130-Curettage-D1_S142.vcf
testData/A/PAT-ID82-DNA-ID131-NORMAL-C2_S11.vcf
testData/A/PAT-ID82-DNA-ID131-NORMAL-E1_S143.vcf
testData/B/PAT-ID100-DNA-ID161-OP-B4_S26.vcf
testData/B/PAT-ID100-DNA-ID161-OP-C4_S27.vcf
testData/B/PAT-ID100-DNA-ID162-NORMAL-D4_S28.vcf
testData/B/PAT-ID101-DNA-ID163-OP-E4_S29.vcf
testData/B/PAT-ID101-DNA-ID163-OP-F4_S30.vcf
testData/B/PAT-ID101-DNA-ID164-NORMAL-G4_S31.vcf
testData/B/PAT-ID95-DNA-ID149-OP-D2_S12.vcf
testData/B/PAT-ID95-DNA-ID149-OP-E2_S13.vcf
testData/B/PAT-ID95-DNA-ID150-NORMAL-F2_S14.vcf
testData/B/PAT-ID96-DNA-ID151-OP-G2_S15.vcf
testData/B/PAT-ID96-DNA-ID151-OP-H2_S16.vcf
testData/B/PAT-ID96-DNA-ID152-NORMAL-A3_S17.vcf
testData/B/PAT-ID96-DNA-ID152-NORMAL-C3_S19.vcf
testData/B/PAT-ID98-DNA-ID156-OP-B3_S18.vcf
testData/B/PAT-ID98-DNA-ID157-NORMAL-D3_S20.vcf
testData/B/PAT-ID99-DNA-ID158-OP-E3_S21.vcf
testData/B/PAT-ID99-DNA-ID158-OP-F3_S22.vcf
testData/B/PAT-ID99-DNA-ID159-Curettage-G3_S23.vcf
testData/B/PAT-ID99-DNA-ID159-Curettage-H3_S24.vcf
testData/B/PAT-ID99-DNA-ID160-NORMAL-A4_S25.vcf
testData/C/PAT-ID105-DNA-ID170-OP-A5_S33.vcf
testData/C/PAT-ID105-DNA-ID170-OP-H4_S32.vcf
testData/C/PAT-ID105-DNA-ID171-NORMAL-B5_S34.vcf
testData/C/PAT-ID108-DNA-ID172-OP-C5_S35.vcf
testData/C/PAT-ID108-DNA-ID172-OP-D5_S36.vcf
testData/C/PAT-ID108-DNA-ID173-NORMAL-E5_S37.vcf
testData/C/PAT-ID109-DNA-ID174-OP-F5_S38.vcf
testData/C/PAT-ID109-DNA-ID174-OP-G5_S39.vcf
testData/C/PAT-ID109-DNA-ID175-NORMAL-H5_S40.vcf
testData/C/PAT-ID110-DNA-ID176-OP-A1_S48.vcf
testData/C/PAT-ID110-DNA-ID176-OP-B1_S49.vcf
testData/C/PAT-ID110-DNA-ID177-Curettage-C1_S50.vcf
testData/C/PAT-ID110-DNA-ID177-Curettage-D1_S51.vcf
testData/C/PAT-ID110-DNA-ID178-NORMAL-E1_S52.vcf
testData/D/PAT-ID111-DNA-ID179-OP-F1_S53.vcf
testData/D/PAT-ID111-DNA-ID179-OP-G1_S54.vcf
testData/D/PAT-ID111-DNA-ID180-Curettage-A2_S56.vcf
testData/D/PAT-ID111-DNA-ID180-Curettage-H1_S55.vcf
testData/D/PAT-ID111-DNA-ID181-NORMAL-B2_S57.vcf
testData/D/PAT-ID112-DNA-ID182-OP-A6_S41.vcf
testData/D/PAT-ID112-DNA-ID182-OP-B6_S42.vcf
testData/D/PAT-ID112-DNA-ID183-NORMAL-C6_S43.vcf
testData/D/PAT-ID114-DNA-ID185-OP-A1_S95.vcf
testData/D/PAT-ID114-DNA-ID185-OP-B1_S96.vcf
testData/D/PAT-ID114-DNA-ID186-Curettage-C1_S97.vcf
testData/D/PAT-ID114-DNA-ID186-Curettage-D1_S98.vcf
testData/D/PAT-ID114-DNA-ID187-NORMAL-E1_S99.vcf
testData/D/PAT-ID116-DNA-ID190-OP-D6_S44.vcf
testData/D/PAT-ID116-DNA-ID190-OP-E6_S45.vcf
testData/D/PAT-ID116-DNA-ID191-NORMAL-F6_S46.vcf
testData/D/PAT-ID117-DNA-ID192-OP-C2_S58.vcf
testData/D/PAT-ID117-DNA-ID192-OP-D2_S59.vcf
testData/D/PAT-ID117-DNA-ID193-NORMAL-E2_S60.vcf
testData/E/PAT-ID118-DNA-ID194-OP-F2_S61.vcf
testData/E/PAT-ID118-DNA-ID194-OP-G2_S62.vcf
testData/E/PAT-ID118-DNA-ID195-NORMAL-H2_S63.vcf
testData/E/PAT-ID119-DNA-ID196-OP-A3_S64.vcf
testData/E/PAT-ID119-DNA-ID196-OP-B3_S65.vcf
testData/E/PAT-ID119-DNA-ID197-NORMAL-C3_S66.vcf
testData/E/PAT-ID120-DNA-ID198-OP-D3_S67.vcf
testData/E/PAT-ID120-DNA-ID198-OP-E3_S68.vcf
testData/E/PAT-ID120-DNA-ID199-NORMAL-F3_S69.vcf
testData/E/PAT-ID121-DNA-ID200-OP-B6_S136.vcf
testData/E/PAT-ID121-DNA-ID200-OP-C6_S137.vcf
testData/E/PAT-ID121-DNA-ID201-Curettage-D6_S138.vcf
testData/E/PAT-ID121-DNA-ID201-Curettage-E6_S139.vcf
testData/E/PAT-ID121-DNA-ID202-NORMAL-F6_S140.vcf
testData/E/PAT-ID128-DNA-ID208-OP-G3_S70.vcf
testData/E/PAT-ID128-DNA-ID208-OP-H3_S71.vcf
testData/E/PAT-ID128-DNA-ID209-NORMAL-A4_S72.vcf
testData/F/PAT-ID129-DNA-ID210-OP-B4_S73.vcf
testData/F/PAT-ID129-DNA-ID210-OP-C4_S74.vcf
testData/F/PAT-ID129-DNA-ID211-NORMAL-D4_S75.vcf
testData/F/PAT-ID132-DNA-ID214-OP-E4_S76.vcf
testData/F/PAT-ID132-DNA-ID214-OP-F4_S77.vcf
testData/F/PAT-ID132-DNA-ID215-NORMAL-G4_S78.vcf
testData/F/PAT-ID133-DNA-ID216-OP-F1_S100.vcf
testData/F/PAT-ID133-DNA-ID216-OP-G1_S101.vcf
testData/F/PAT-ID133-DNA-ID217-NORMAL-H1_S102.vcf
tests/testthat.R
tests/testthat/test-checkFC.R
tests/testthat/test-filterPassDepth.R
tests/testthat/test-filterQualityFrequency.R
tests/testthat/test-getPatientID.R
tests/testthat/test-labelMutationGroup.R
tests/testthat/test-labelTumorType.R
tests/testthat/test-notMutationGroupException.R
tests/testthat/test-onceN.R
tests/testthat/test-onceT1.R
tests/testthat/test-onceT2.R
tests/testthat/test-onlyRepetitivePos.R
tests/testthat/test-processAmpliconInfo.R
tests/testthat/test-splitINFO.R
tests/testthat/test-twiceT1.R
tests/testthat/test-twiceT2.R
