Supplement.md
In DHLab-CGU/emr: An analysis tool for diagnosis and procedure records
Usage of dxpr Package
I. Data integration
head(sampleDxFile)
#> ID ICD Date Version
#> 1: A2 Z992 2020-05-22 10
#> 2: A5 Z992 2020-01-24 10
#> 3: A8 Z992 2015-10-27 10
#> 4: A13 Z992 2020-04-26 10
#> 5: A13 Z992 2025-02-02 10
#> 6: A15 Z992 2023-05-12 10
1. Data standardization
# ICD to uniform short format
ICD_Short <- icdDxDecimalToShort(dxDataFile = sampleDxFile,
icdColName = ICD,
dateColName = Date,
icd10usingDate = "2015/10/01")
#> Wrong ICD format: total 9 ICD codes (the number of occurrences is in brackets)
#> c("A0.11 (20)", "E114 (8)", "Z9.90 (6)", "F42 (6)", "001 (5)", "75.52 (4)", "755.2 (3)", "123.45 (3)", "7552 (2)")
#>
#> Wrong ICD version: total 7 ICD codes (the number of occurrences is in brackets)
#> c("V27.0 (18)", "A01.05 (8)", "42761 (7)", "V24.1 (6)", "A0105 (5)", "E03.0 (4)", "650 (4)")
#>
#> Warning: The ICD mentioned above matches to "NA" due to the format or other
#> issues.
#> Warning: "Wrong ICD format" means the ICD has wrong format
#> Warning: "Wrong ICD version" means the ICD classify to wrong ICD version (cause
#> the "icd10usingDate" or other issues)
head(ICD_Short$ICD)
#> ICD
#> 1: Z992
#> 2: Z992
#> 3: Z992
#> 4: Z992
#> 5: Z992
#> 6: Z992
tail(ICD_Short$Error)
#> ICD count IcdVersionInFile WrongType Suggestion
#> 1: 75.52 4 ICD 9 Wrong format
#> 2: E03.0 4 ICD 9 Wrong version
#> 3: 650 4 ICD 10 Wrong version
#> 4: 123.45 3 ICD 10 Wrong format
#> 5: 755.2 3 ICD 9 Wrong format 755.29
#> 6: 7552 2 ICD 9 Wrong format 75529
sampleDxFile$Decimal <- ICD_Short$ICD
head(sampleDxFile)
#> ID ICD Date Version Decimal
#> 1: A2 Z992 2020-05-22 10 Z992
#> 2: A5 Z992 2020-01-24 10 Z992
#> 3: A8 Z992 2015-10-27 10 Z992
#> 4: A13 Z992 2020-04-26 10 Z992
#> 5: A13 Z992 2025-02-02 10 Z992
#> 6: A15 Z992 2023-05-12 10 Z992
2. Data grouping
# ICD to level 2 CCS description of multiple-level CCS
CCSlvl_description <- icdDxToCCSLvl(dxDataFile = sampleDxFile,
idColName = ID,
icdColName = ICD,
dateColName = Date,
icd10usingDate = "2015-10-01",
CCSLevel = 2,
isDescription = TRUE)
head(setorder(CCSlvl_description$groupedDT, "ID"))
#> Short ID ICD Date CCS_LVL_2_LABEL
#> 1: 5855 A0 5855 2013-12-20 Diseases of the urinary system
#> 2: V4511 A0 V4511 2012-04-05 Diseases of the urinary system
#> 3: V560 A0 V560 2010-03-28 Diseases of the urinary system
#> 4: 5853 A0 5853 2010-10-29 Diseases of the urinary system
#> 5: 5856 A0 5856 2009-07-25 Diseases of the urinary system
#> 6: 001 A0 001 2014-11-05 <NA>
head(CCSlvl_description$summarised_groupedDT)
#> ID CCS_LVL_2_LABEL firstCaseDate endCaseDate count period
#> 1: A0 Diseases of the urinary system 2009-07-25 2013-12-20 5 1609 days
#> 2: A1 Diseases of the urinary system 2006-11-29 2014-09-24 5 2856 days
#> 3: A10 Diseases of the urinary system 2007-11-04 2012-07-30 5 1730 days
#> 4: A11 Diseases of the urinary system 2008-03-09 2011-09-03 5 1273 days
#> 5: A12 Diseases of the urinary system 2006-05-14 2015-06-29 5 3333 days
#> 6: A13 Diseases of the urinary system 2006-04-29 2025-02-02 5 6854 days
## ICD to pheWAS
pheWAS <- icdDxToPheWAS(dxDataFile = sampleDxFile,
idColName = ID,
icdColName = ICD,
dateColName = Date,
icd10usingDate = "2015-10-01",
isDescription = FALSE)
head(setorder(pheWAS$groupedDT, "ID"))
#> Decimal ID ICD Date PheCode
#> 1: 585.5 A0 5855 2013-12-20 585.32
#> 2: V45.11 A0 V4511 2012-04-05 585.31
#> 3: V56.0 A0 V560 2010-03-28 585.31
#> 4: 585.3 A0 5853 2010-10-29 585.33
#> 5: 585.6 A0 5856 2009-07-25 585.32
#> 6: 001 A0 001 2014-11-05 008
head(setorder(pheWAS$summarised_groupedDT, "ID"))
#> ID PheCode firstCaseDate endCaseDate count period
#> 1: A0 585.32 2009-07-25 2013-12-20 2 1609 days
#> 2: A0 585.31 2010-03-28 2012-04-05 2 739 days
#> 3: A0 585.33 2010-10-29 2010-10-29 1 0 days
#> 4: A0 008 2014-11-05 2014-11-05 1 0 days
#> 5: A1 585.32 2006-11-29 2013-04-28 3 2342 days
#> 6: A1 585.33 2014-09-24 2014-09-24 1 0 days
# ICD to Comorbidity: Elixhauser
ELIX <- icdDxToComorbid(dxDataFile = sampleDxFile,
idColName = ID,
icdColName = ICD,
dateColName = Date,
icd10usingDate = "2015-10-01",
comorbidMethod = ELIX)
head(setorder(ELIX$groupedDT, "ID"))
#> Short ID ICD Date Comorbidity
#> 1: 5855 A0 5855 2013-12-20 RENLFAIL
#> 2: V4511 A0 V4511 2012-04-05 RENLFAIL
#> 3: V560 A0 V560 2010-03-28 RENLFAIL
#> 4: 5853 A0 5853 2010-10-29 RENLFAIL
#> 5: 5856 A0 5856 2009-07-25 RENLFAIL
#> 6: 001 A0 001 2014-11-05 <NA>
head(ELIX$summarised_groupedDT)
#> ID Comorbidity firstCaseDate endCaseDate count period
#> 1: A0 RENLFAIL 2009-07-25 2013-12-20 5 1609 days
#> 2: A1 RENLFAIL 2006-11-29 2014-09-24 5 2856 days
#> 3: A10 RENLFAIL 2007-11-04 2012-07-30 5 1730 days
#> 4: A11 RENLFAIL 2008-03-09 2011-09-03 5 1273 days
#> 5: A12 RENLFAIL 2006-05-14 2015-06-29 5 3333 days
#> 6: A13 RENLFAIL 2006-04-29 2025-02-02 5 6854 days
# ICD to Comorbidity: AHRQ
AHRQ <- icdDxToComorbid(dxDataFile = sampleDxFile,
idColName = ID,
icdColName = ICD,
dateColName = Date,
icd10usingDate = "2015-10-01",
comorbidMethod = ahrq)
head(setorder(AHRQ$groupedDT, "ID"))
#> Short ID ICD Date Comorbidity
#> 1: 5855 A0 5855 2013-12-20 Renal
#> 2: V4511 A0 V4511 2012-04-05 Renal
#> 3: V560 A0 V560 2010-03-28 Renal
#> 4: 5853 A0 5853 2010-10-29 Renal
#> 5: 5856 A0 5856 2009-07-25 Renal
#> 6: 001 A0 001 2014-11-05 <NA>
head(AHRQ$summarised_groupedDT)
#> ID Comorbidity firstCaseDate endCaseDate count period
#> 1: A0 Renal 2009-07-25 2013-12-20 5 1609 days
#> 2: A1 Renal 2006-11-29 2014-09-24 5 2856 days
#> 3: A10 Renal 2007-11-04 2012-07-30 5 1730 days
#> 4: A11 Renal 2008-03-09 2011-09-03 5 1273 days
#> 5: A12 Renal 2006-05-14 2015-06-29 5 3333 days
#> 6: A13 Renal 2006-04-29 2025-02-02 5 6854 days
# ICD to Comorbidity: Charlson
Charlson <- icdDxToComorbid(dxDataFile = sampleDxFile,
idColName = ID,
icdColName = ICD,
dateColName = Date,
icd10usingDate = "2015-10-01",
comorbidMethod = Charlson)
head(setorder(Charlson$groupedDT, "ID"))
#> Short ID ICD Date Comorbidity
#> 1: 5855 A0 5855 2013-12-20 RD
#> 2: V4511 A0 V4511 2012-04-05 RD
#> 3: V560 A0 V560 2010-03-28 RD
#> 4: 5853 A0 5853 2010-10-29 RD
#> 5: 5856 A0 5856 2009-07-25 RD
#> 6: 001 A0 001 2014-11-05 <NA>
head(Charlson$summarised_groupedDT)
#> ID Comorbidity firstCaseDate endCaseDate count period
#> 1: A0 RD 2009-07-25 2013-12-20 5 1609 days
#> 2: A1 RD 2006-11-29 2014-09-24 5 2856 days
#> 3: A10 RD 2007-11-04 2012-07-30 5 1730 days
#> 4: A11 RD 2008-03-09 2011-09-03 5 1273 days
#> 5: A11 DIAB_C 2015-12-16 2015-12-16 1 0 days
#> 6: A12 RD 2006-05-14 2015-06-29 5 3333 days
# ICD to self-defined grouping method: precise matching
groupingTable <- data.table(Group = rep("Chronic kidney disease",6),
ICD = c("N181","5853","5854","5855","5856","5859"))
groupingTable
#> Group ICD
#> 1: Chronic kidney disease N181
#> 2: Chronic kidney disease 5853
#> 3: Chronic kidney disease 5854
#> 4: Chronic kidney disease 5855
#> 5: Chronic kidney disease 5856
#> 6: Chronic kidney disease 5859
CustomGroup <- icdDxToCustom(dxDataFile = sampleDxFile,
idColName = ID,
icdColName = ICD,
dateColName = Date,
customGroupingTable = groupingTable)
head(setorder(CustomGroup$groupedDT, "ID"))
#> ICD ID Date Group
#> 1: 5855 A0 2013-12-20 Chronic kidney disease
#> 2: V4511 A0 2012-04-05 <NA>
#> 3: V560 A0 2010-03-28 <NA>
#> 4: 5853 A0 2010-10-29 Chronic kidney disease
#> 5: 5856 A0 2009-07-25 Chronic kidney disease
#> 6: 001 A0 2014-11-05 <NA>
head(CustomGroup$summarised_groupedDT)
#> ID Group firstCaseDate endCaseDate count period
#> 1: A0 Chronic kidney disease 2009-07-25 2013-12-20 3 1609 days
#> 2: A1 Chronic kidney disease 2006-11-29 2014-09-24 4 2856 days
#> 3: A10 Chronic kidney disease 2007-11-04 2007-11-04 1 0 days
#> 4: A11 Chronic kidney disease 2008-03-09 2010-02-21 2 714 days
#> 5: A12 Chronic kidney disease 2006-05-14 2011-02-25 3 1748 days
#> 6: A13 Chronic kidney disease 2006-04-29 2010-02-21 2 1394 days
# ICD to self-defined grouping method: fuzzy matching
grepTable <- data.table(Group = "Chronic kidney disease",
grepIcd = "^585|^N18")
grepTable
#> Group grepIcd
#> 1: Chronic kidney disease ^585|^N18
CustomGrepGroup <- icdDxToCustomGrep(dxDataFile = sampleDxFile,
idColName = ID,
icdColName = ICD,
dateColName = Date,
customGroupingTable = grepTable)
head(setorder(CustomGrepGroup$groupedDT, "ID"))
#> ID ICD Date GrepedGroup
#> 1: A0 5855 2013-12-20 Chronic kidney disease
#> 2: A0 V4511 2012-04-05 <NA>
#> 3: A0 V560 2010-03-28 <NA>
#> 4: A0 5853 2010-10-29 Chronic kidney disease
#> 5: A0 5856 2009-07-25 Chronic kidney disease
#> 6: A0 001 2014-11-05 <NA>
II. Data wrangling
1. Case selection
# Select cases by ICD condition "^585"
Case <- selectCases(dxDataFile = sampleDxFile,
idColName = ID,
icdColName = ICD,
dateColName = Date,
icd10usingDate = "2015/10/01",
groupDataType = icd,
caseCondition = "^585",
caseCount = 2,
periodRange = c(30, 365))
head(Case)
#> ID selectedCase count firstCaseDate endCaseDate period MostCommonICD
#> 1: A1 Selected 4 2006-11-29 2014-09-24 2856 days 5855
#> 2: A12 Selected* 3 2006-05-14 2011-02-25 1748 days 5859
#> 3: A13 Selected* 2 2006-04-29 2010-02-21 1394 days 5855
#> 4: A18 Selected* 2 2007-04-05 2012-02-10 1772 days 5855
#> 5: A2 Selected* 3 2011-09-20 2015-01-06 1204 days 5855
#> 6: A0 Selected* 3 2009-07-25 2013-12-20 1609 days 5856
#> MostCommonICDCount
#> 1: 2
#> 2: 2
#> 3: 2
#> 4: 2
#> 5: 2
#> 6: 1
tail(Case)
#> ID selectedCase count firstCaseDate endCaseDate period MostCommonICD
#> 1: D3 non-Selected NA <NA> <NA> NA days <NA>
#> 2: D4 non-Selected NA <NA> <NA> NA days <NA>
#> 3: D5 non-Selected NA <NA> <NA> NA days <NA>
#> 4: D6 non-Selected NA <NA> <NA> NA days <NA>
#> 5: D7 non-Selected NA <NA> <NA> NA days <NA>
#> 6: D8 non-Selected NA <NA> <NA> NA days <NA>
#> MostCommonICDCount
#> 1: NA
#> 2: NA
#> 3: NA
#> 4: NA
#> 5: NA
#> 6: NA
# Select cases by AHRQ comorbidity condition "Renal"
Case <- selectCases(dxDataFile = sampleDxFile,
idColName = ID,
icdColName = ICD,
dateColName = Date,
icd10usingDate = "2015/10/01",
groupDataType = ahrq,
isDescription = FALSE,
caseCondition = "Renal",
caseCount = 1,
periodRange = c(30, 365))
head(Case)
#> ID selectedCase count firstCaseDate endCaseDate period MostCommonICD
#> 1: A3 Selected 5 2008-07-08 2014-02-24 2057 days V420
#> 2: A1 Selected 5 2006-11-29 2014-09-24 2856 days 5855
#> 3: A10 Selected 5 2007-11-04 2012-07-30 1730 days V5631
#> 4: A12 Selected 5 2006-05-14 2015-06-29 3333 days 5859
#> 5: A13 Selected 5 2006-04-29 2025-02-02 6854 days 5855
#> 6: A15 Selected 5 2007-05-25 2023-05-12 5831 days V5631
#> MostCommonICDCount
#> 1: 3
#> 2: 2
#> 3: 2
#> 4: 2
#> 5: 2
#> 6: 2
# Select cases by CCS Level 2 condition "Diseases of the urinary system"
Case <- selectCases(dxDataFile = sampleDxFile,
idColName = ID,
icdColName = ICD,
dateColName = Date,
icd10usingDate = "2015/10/01",
groupDataType = ccslvl2,
isDescription = TRUE,
caseCondition = "Diseases of the urinary system",
caseCount = 1,
periodRange = c(30, 365))
head(Case)
#> ID selectedCase count firstCaseDate endCaseDate period MostCommonICD
#> 1: A3 Selected 5 2008-07-08 2014-02-24 2057 days V420
#> 2: A1 Selected 5 2006-11-29 2014-09-24 2856 days 5855
#> 3: A10 Selected 5 2007-11-04 2012-07-30 1730 days V5631
#> 4: A12 Selected 5 2006-05-14 2015-06-29 3333 days 5859
#> 5: A13 Selected 5 2006-04-29 2025-02-02 6854 days 5855
#> 6: A15 Selected 5 2007-05-25 2023-05-12 5831 days V5631
#> MostCommonICDCount
#> 1: 3
#> 2: 2
#> 3: 2
#> 4: 2
#> 5: 2
#> 6: 2
2. Condition era generation
# get era by the comorbidity condition ELIX
Era <- getConditionEra(dxDataFile = sampleDxFile,
idColName = ID,
icdColName = ICD,
dateColName = Date,
icd10usingDate = "2015/10/01",
groupDataType = ELIX,
isDescription = TRUE,
gapDate = 30)
head(Era)
#> ID Description era firstCaseDate endCaseDate count period
#> 1: A0 Renal failure 1 2009-07-25 2009-07-25 1 0 days
#> 2: A0 Renal failure 2 2010-03-28 2010-03-28 1 0 days
#> 3: A0 Renal failure 3 2010-10-29 2010-10-29 1 0 days
#> 4: A0 Renal failure 4 2012-04-05 2012-04-05 1 0 days
#> 5: A0 Renal failure 5 2013-12-20 2013-12-20 1 0 days
#> 6: A1 Renal failure 1 2006-11-29 2006-11-29 1 0 days
3. Analysis ready data generation
# generate analysis ready data mapped with case and Control Group
CHARLSON <- icdDxToComorbid(dxDataFile = sampleDxFile,
idColName = ID,
icdColName = ICD,
dateColName = Date,
icd10usingDate = "2015-10-01",
comorbidMethod = CHARLSON)
head(CHARLSON$groupedDT)
#> Short ID ICD Date Comorbidity
#> 1: Z992 A2 Z992 2020-05-22 RD
#> 2: Z992 A5 Z992 2020-01-24 RD
#> 3: Z992 A8 Z992 2015-10-27 RD
#> 4: Z992 A13 Z992 2020-04-26 RD
#> 5: Z992 A13 Z992 2025-02-02 RD
#> 6: Z992 A15 Z992 2023-05-12 RD
selectedCaseFile <- selectCases(dxDataFile = sampleDxFile,
idColName = ID,
icdColName = ICD,
dateColName = Date,
icd10usingDate = "2015/10/01",
groupDataType = ccs,
caseCondition = "11",
isDescription = FALSE,
caseCount = 1)
head(selectedCaseFile)
#> ID selectedCase count firstCaseDate endCaseDate period MostCommonICD
#> 1: C0 Selected 2 2016-07-05 2025-02-21 3153 days C048
#> 2: C1 Selected 1 2018-02-13 2018-02-13 0 days C320
#> 3: C2 Selected 1 2016-09-09 2016-09-09 0 days C006
#> 4: C4 Selected 1 2022-10-23 2022-10-23 0 days C130
#> 5: D4 Selected 1 2020-10-06 2020-10-06 0 days I69942
#> 6: A2 non-Selected NA <NA> <NA> NA days <NA>
#> MostCommonICDCount
#> 1: 1
#> 2: 1
#> 3: 1
#> 4: 1
#> 5: 1
#> 6: NA
groupedDataWide <- groupedDataLongToWide(dxDataFile = CHARLSON$groupedDT,
idColName = ID,
categoryColName = Comorbidity,
dateColName = Date,
reDup = TRUE,
numericOrBinary = N,
selectedCaseFile = selectedCaseFile)
tail(groupedDataWide)
#> ID CANCER CEVD COPD DIAB_C MSLD PARA PUD PVD RD Rheum selectedCase
#> 1: D3 0 0 0 0 0 0 0 1 0 0 non-Selected
#> 2: D4 1 1 0 1 0 0 0 0 0 0 Selected
#> 3: D5 1 0 1 1 0 0 0 0 0 1 non-Selected
#> 4: D6 0 0 0 0 0 0 0 0 0 0 non-Selected
#> 5: D7 1 0 0 1 0 0 0 0 0 1 non-Selected
#> 6: D8 1 0 0 0 0 1 0 1 0 0 non-Selected
III. Visualization
# Bar chart of diagnostic categories – case and control groups
selectedCaseFile <- selectCases(dxDataFile = sampleDxFile,
idColName = ID,
icdColName = ICD,
dateColName = Date,
icd10usingDate = "2015/10/01",
groupDataType = ccs,
caseCondition = "11",
isDescription = FALSE,
caseCount = 1)
groupedDataWide <- groupedDataLongToWide(dxDataFile = ELIX$groupedDT,
idColName = ID,
categoryColName = Comorbidity,
dateColName = Date,
reDup = TRUE,
numericOrBinary = B,
count = 2,
selectedCaseFile = selectedCaseFile)
plot <- plotDiagCat(groupedDataWide = groupedDataWide,
idColName = ID,
groupColName = selectedCase,
topN = 10,
limitFreq = 0.01,
pvalue = 0.05)
plot$graph
plot$sigCate
#> DiagnosticCategory Group N Percentage
#> 1: TUMOR non-Selected 1 3.03
#> 2: TUMOR Selected 4 80.00
IV. Procedure
head(samplePrFile)
#> ID ICD Date
#> 1: B 5681 2008-01-14
#> 2: A 9774 2009-01-11
#> 3: B 44.99 2009-05-10
#> 4: C 07.59 2009-01-21
#> 5: B 0205 2008-07-06
#> 6: B 8812 2007-06-27
1. Code classification
# CCS single level classification
CCS <- icdPrToCCS (prDataFile = samplePrFile,
idColName = ID,
icdColName = ICD,
dateColName = Date,
icd10usingDate = "2015-10-01",
isDescription = TRUE)
head(CCS$groupedDT)
#> Short ID ICD Date CCS_CATEGORY_DESCRIPTION
#> 1: 5681 B 5681 2008-01-14 Other OR therapeutic procedures of urinary tract
#> 2: 9774 A 9774 2009-01-11 Other non-OR therapeutic procedures; female organs
#> 3: 4499 B 44.99 2009-05-10 Other OR upper GI therapeutic procedures
#> 4: 0759 C 07.59 2009-01-21 Therapeutic endocrine procedures
#> 5: 0205 B 0205 2008-07-06 Other OR therapeutic nervous system procedures
#> 6: 8812 B 8812 2007-06-27 Other diagnostic radiology and related techniques
# ICD to CCS multiple level 1
CCSlvl <- icdPrToCCSLvl(prDataFile = samplePrFile,
idColName = ID,
icdColName = ICD,
dateColName = Date,
icd10usingDate = "2015-10-01",
CCSLevel = 2,
isDescription = FALSE)
head(CCSlvl$groupedDT)
#> Short ID ICD Date CCS_LVL_2
#> 1: 5681 B 5681 2008-01-14 10.11
#> 2: 9774 A 9774 2009-01-11 12.12
#> 3: 4499 B 44.99 2009-05-10 9.26
#> 4: 0759 C 07.59 2009-01-21 2.3
#> 5: 0205 B 0205 2008-07-06 1.9
#> 6: 8812 B 8812 2007-06-27 16.37
# Procedure class
ProcedureClass <- icdPrToProcedureClass(prDataFile = samplePrFile,
idColName = ID,
icdColName = ICD,
dateColName = Date,
icd10usingDate = "2015-10-01",
isDescription = FALSE)
head(ProcedureClass$groupedDT)
#> Short ID ICD Date PROCEDURE_CLASS
#> 1: 5681 B 5681 2008-01-14 4
#> 2: 9774 A 9774 2009-01-11 2
#> 3: 4499 B 44.99 2009-05-10 4
#> 4: 0759 C 07.59 2009-01-21 4
#> 5: 0205 B 0205 2008-07-06 4
#> 6: 8812 B 8812 2007-06-27 1
DHLab-CGU/emr documentation built on Sept. 2, 2023, 9:16 p.m.
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Usage of dxpr Package
I. Data integration
head(sampleDxFile)
#> ID ICD Date Version
#> 1: A2 Z992 2020-05-22 10
#> 2: A5 Z992 2020-01-24 10
#> 3: A8 Z992 2015-10-27 10
#> 4: A13 Z992 2020-04-26 10
#> 5: A13 Z992 2025-02-02 10
#> 6: A15 Z992 2023-05-12 10
1. Data standardization
# ICD to uniform short format
ICD_Short <- icdDxDecimalToShort(dxDataFile = sampleDxFile,
icdColName = ICD,
dateColName = Date,
icd10usingDate = "2015/10/01")
#> Wrong ICD format: total 9 ICD codes (the number of occurrences is in brackets)
#> c("A0.11 (20)", "E114 (8)", "Z9.90 (6)", "F42 (6)", "001 (5)", "75.52 (4)", "755.2 (3)", "123.45 (3)", "7552 (2)")
#>
#> Wrong ICD version: total 7 ICD codes (the number of occurrences is in brackets)
#> c("V27.0 (18)", "A01.05 (8)", "42761 (7)", "V24.1 (6)", "A0105 (5)", "E03.0 (4)", "650 (4)")
#>
#> Warning: The ICD mentioned above matches to "NA" due to the format or other
#> issues.
#> Warning: "Wrong ICD format" means the ICD has wrong format
#> Warning: "Wrong ICD version" means the ICD classify to wrong ICD version (cause
#> the "icd10usingDate" or other issues)
head(ICD_Short$ICD)
#> ICD
#> 1: Z992
#> 2: Z992
#> 3: Z992
#> 4: Z992
#> 5: Z992
#> 6: Z992
tail(ICD_Short$Error)
#> ICD count IcdVersionInFile WrongType Suggestion
#> 1: 75.52 4 ICD 9 Wrong format
#> 2: E03.0 4 ICD 9 Wrong version
#> 3: 650 4 ICD 10 Wrong version
#> 4: 123.45 3 ICD 10 Wrong format
#> 5: 755.2 3 ICD 9 Wrong format 755.29
#> 6: 7552 2 ICD 9 Wrong format 75529
sampleDxFile$Decimal <- ICD_Short$ICD
head(sampleDxFile)
#> ID ICD Date Version Decimal
#> 1: A2 Z992 2020-05-22 10 Z992
#> 2: A5 Z992 2020-01-24 10 Z992
#> 3: A8 Z992 2015-10-27 10 Z992
#> 4: A13 Z992 2020-04-26 10 Z992
#> 5: A13 Z992 2025-02-02 10 Z992
#> 6: A15 Z992 2023-05-12 10 Z992
2. Data grouping
# ICD to level 2 CCS description of multiple-level CCS
CCSlvl_description <- icdDxToCCSLvl(dxDataFile = sampleDxFile,
idColName = ID,
icdColName = ICD,
dateColName = Date,
icd10usingDate = "2015-10-01",
CCSLevel = 2,
isDescription = TRUE)
head(setorder(CCSlvl_description$groupedDT, "ID"))
#> Short ID ICD Date CCS_LVL_2_LABEL
#> 1: 5855 A0 5855 2013-12-20 Diseases of the urinary system
#> 2: V4511 A0 V4511 2012-04-05 Diseases of the urinary system
#> 3: V560 A0 V560 2010-03-28 Diseases of the urinary system
#> 4: 5853 A0 5853 2010-10-29 Diseases of the urinary system
#> 5: 5856 A0 5856 2009-07-25 Diseases of the urinary system
#> 6: 001 A0 001 2014-11-05 <NA>
head(CCSlvl_description$summarised_groupedDT)
#> ID CCS_LVL_2_LABEL firstCaseDate endCaseDate count period
#> 1: A0 Diseases of the urinary system 2009-07-25 2013-12-20 5 1609 days
#> 2: A1 Diseases of the urinary system 2006-11-29 2014-09-24 5 2856 days
#> 3: A10 Diseases of the urinary system 2007-11-04 2012-07-30 5 1730 days
#> 4: A11 Diseases of the urinary system 2008-03-09 2011-09-03 5 1273 days
#> 5: A12 Diseases of the urinary system 2006-05-14 2015-06-29 5 3333 days
#> 6: A13 Diseases of the urinary system 2006-04-29 2025-02-02 5 6854 days
## ICD to pheWAS
pheWAS <- icdDxToPheWAS(dxDataFile = sampleDxFile,
idColName = ID,
icdColName = ICD,
dateColName = Date,
icd10usingDate = "2015-10-01",
isDescription = FALSE)
head(setorder(pheWAS$groupedDT, "ID"))
#> Decimal ID ICD Date PheCode
#> 1: 585.5 A0 5855 2013-12-20 585.32
#> 2: V45.11 A0 V4511 2012-04-05 585.31
#> 3: V56.0 A0 V560 2010-03-28 585.31
#> 4: 585.3 A0 5853 2010-10-29 585.33
#> 5: 585.6 A0 5856 2009-07-25 585.32
#> 6: 001 A0 001 2014-11-05 008
head(setorder(pheWAS$summarised_groupedDT, "ID"))
#> ID PheCode firstCaseDate endCaseDate count period
#> 1: A0 585.32 2009-07-25 2013-12-20 2 1609 days
#> 2: A0 585.31 2010-03-28 2012-04-05 2 739 days
#> 3: A0 585.33 2010-10-29 2010-10-29 1 0 days
#> 4: A0 008 2014-11-05 2014-11-05 1 0 days
#> 5: A1 585.32 2006-11-29 2013-04-28 3 2342 days
#> 6: A1 585.33 2014-09-24 2014-09-24 1 0 days
# ICD to Comorbidity: Elixhauser
ELIX <- icdDxToComorbid(dxDataFile = sampleDxFile,
idColName = ID,
icdColName = ICD,
dateColName = Date,
icd10usingDate = "2015-10-01",
comorbidMethod = ELIX)
head(setorder(ELIX$groupedDT, "ID"))
#> Short ID ICD Date Comorbidity
#> 1: 5855 A0 5855 2013-12-20 RENLFAIL
#> 2: V4511 A0 V4511 2012-04-05 RENLFAIL
#> 3: V560 A0 V560 2010-03-28 RENLFAIL
#> 4: 5853 A0 5853 2010-10-29 RENLFAIL
#> 5: 5856 A0 5856 2009-07-25 RENLFAIL
#> 6: 001 A0 001 2014-11-05 <NA>
head(ELIX$summarised_groupedDT)
#> ID Comorbidity firstCaseDate endCaseDate count period
#> 1: A0 RENLFAIL 2009-07-25 2013-12-20 5 1609 days
#> 2: A1 RENLFAIL 2006-11-29 2014-09-24 5 2856 days
#> 3: A10 RENLFAIL 2007-11-04 2012-07-30 5 1730 days
#> 4: A11 RENLFAIL 2008-03-09 2011-09-03 5 1273 days
#> 5: A12 RENLFAIL 2006-05-14 2015-06-29 5 3333 days
#> 6: A13 RENLFAIL 2006-04-29 2025-02-02 5 6854 days
# ICD to Comorbidity: AHRQ
AHRQ <- icdDxToComorbid(dxDataFile = sampleDxFile,
idColName = ID,
icdColName = ICD,
dateColName = Date,
icd10usingDate = "2015-10-01",
comorbidMethod = ahrq)
head(setorder(AHRQ$groupedDT, "ID"))
#> Short ID ICD Date Comorbidity
#> 1: 5855 A0 5855 2013-12-20 Renal
#> 2: V4511 A0 V4511 2012-04-05 Renal
#> 3: V560 A0 V560 2010-03-28 Renal
#> 4: 5853 A0 5853 2010-10-29 Renal
#> 5: 5856 A0 5856 2009-07-25 Renal
#> 6: 001 A0 001 2014-11-05 <NA>
head(AHRQ$summarised_groupedDT)
#> ID Comorbidity firstCaseDate endCaseDate count period
#> 1: A0 Renal 2009-07-25 2013-12-20 5 1609 days
#> 2: A1 Renal 2006-11-29 2014-09-24 5 2856 days
#> 3: A10 Renal 2007-11-04 2012-07-30 5 1730 days
#> 4: A11 Renal 2008-03-09 2011-09-03 5 1273 days
#> 5: A12 Renal 2006-05-14 2015-06-29 5 3333 days
#> 6: A13 Renal 2006-04-29 2025-02-02 5 6854 days
# ICD to Comorbidity: Charlson
Charlson <- icdDxToComorbid(dxDataFile = sampleDxFile,
idColName = ID,
icdColName = ICD,
dateColName = Date,
icd10usingDate = "2015-10-01",
comorbidMethod = Charlson)
head(setorder(Charlson$groupedDT, "ID"))
#> Short ID ICD Date Comorbidity
#> 1: 5855 A0 5855 2013-12-20 RD
#> 2: V4511 A0 V4511 2012-04-05 RD
#> 3: V560 A0 V560 2010-03-28 RD
#> 4: 5853 A0 5853 2010-10-29 RD
#> 5: 5856 A0 5856 2009-07-25 RD
#> 6: 001 A0 001 2014-11-05 <NA>
head(Charlson$summarised_groupedDT)
#> ID Comorbidity firstCaseDate endCaseDate count period
#> 1: A0 RD 2009-07-25 2013-12-20 5 1609 days
#> 2: A1 RD 2006-11-29 2014-09-24 5 2856 days
#> 3: A10 RD 2007-11-04 2012-07-30 5 1730 days
#> 4: A11 RD 2008-03-09 2011-09-03 5 1273 days
#> 5: A11 DIAB_C 2015-12-16 2015-12-16 1 0 days
#> 6: A12 RD 2006-05-14 2015-06-29 5 3333 days
# ICD to self-defined grouping method: precise matching
groupingTable <- data.table(Group = rep("Chronic kidney disease",6),
ICD = c("N181","5853","5854","5855","5856","5859"))
groupingTable
#> Group ICD
#> 1: Chronic kidney disease N181
#> 2: Chronic kidney disease 5853
#> 3: Chronic kidney disease 5854
#> 4: Chronic kidney disease 5855
#> 5: Chronic kidney disease 5856
#> 6: Chronic kidney disease 5859
CustomGroup <- icdDxToCustom(dxDataFile = sampleDxFile,
idColName = ID,
icdColName = ICD,
dateColName = Date,
customGroupingTable = groupingTable)
head(setorder(CustomGroup$groupedDT, "ID"))
#> ICD ID Date Group
#> 1: 5855 A0 2013-12-20 Chronic kidney disease
#> 2: V4511 A0 2012-04-05 <NA>
#> 3: V560 A0 2010-03-28 <NA>
#> 4: 5853 A0 2010-10-29 Chronic kidney disease
#> 5: 5856 A0 2009-07-25 Chronic kidney disease
#> 6: 001 A0 2014-11-05 <NA>
head(CustomGroup$summarised_groupedDT)
#> ID Group firstCaseDate endCaseDate count period
#> 1: A0 Chronic kidney disease 2009-07-25 2013-12-20 3 1609 days
#> 2: A1 Chronic kidney disease 2006-11-29 2014-09-24 4 2856 days
#> 3: A10 Chronic kidney disease 2007-11-04 2007-11-04 1 0 days
#> 4: A11 Chronic kidney disease 2008-03-09 2010-02-21 2 714 days
#> 5: A12 Chronic kidney disease 2006-05-14 2011-02-25 3 1748 days
#> 6: A13 Chronic kidney disease 2006-04-29 2010-02-21 2 1394 days
# ICD to self-defined grouping method: fuzzy matching
grepTable <- data.table(Group = "Chronic kidney disease",
grepIcd = "^585|^N18")
grepTable
#> Group grepIcd
#> 1: Chronic kidney disease ^585|^N18
CustomGrepGroup <- icdDxToCustomGrep(dxDataFile = sampleDxFile,
idColName = ID,
icdColName = ICD,
dateColName = Date,
customGroupingTable = grepTable)
head(setorder(CustomGrepGroup$groupedDT, "ID"))
#> ID ICD Date GrepedGroup
#> 1: A0 5855 2013-12-20 Chronic kidney disease
#> 2: A0 V4511 2012-04-05 <NA>
#> 3: A0 V560 2010-03-28 <NA>
#> 4: A0 5853 2010-10-29 Chronic kidney disease
#> 5: A0 5856 2009-07-25 Chronic kidney disease
#> 6: A0 001 2014-11-05 <NA>
II. Data wrangling
1. Case selection
# Select cases by ICD condition "^585"
Case <- selectCases(dxDataFile = sampleDxFile,
idColName = ID,
icdColName = ICD,
dateColName = Date,
icd10usingDate = "2015/10/01",
groupDataType = icd,
caseCondition = "^585",
caseCount = 2,
periodRange = c(30, 365))
head(Case)
#> ID selectedCase count firstCaseDate endCaseDate period MostCommonICD
#> 1: A1 Selected 4 2006-11-29 2014-09-24 2856 days 5855
#> 2: A12 Selected* 3 2006-05-14 2011-02-25 1748 days 5859
#> 3: A13 Selected* 2 2006-04-29 2010-02-21 1394 days 5855
#> 4: A18 Selected* 2 2007-04-05 2012-02-10 1772 days 5855
#> 5: A2 Selected* 3 2011-09-20 2015-01-06 1204 days 5855
#> 6: A0 Selected* 3 2009-07-25 2013-12-20 1609 days 5856
#> MostCommonICDCount
#> 1: 2
#> 2: 2
#> 3: 2
#> 4: 2
#> 5: 2
#> 6: 1
tail(Case)
#> ID selectedCase count firstCaseDate endCaseDate period MostCommonICD
#> 1: D3 non-Selected NA <NA> <NA> NA days <NA>
#> 2: D4 non-Selected NA <NA> <NA> NA days <NA>
#> 3: D5 non-Selected NA <NA> <NA> NA days <NA>
#> 4: D6 non-Selected NA <NA> <NA> NA days <NA>
#> 5: D7 non-Selected NA <NA> <NA> NA days <NA>
#> 6: D8 non-Selected NA <NA> <NA> NA days <NA>
#> MostCommonICDCount
#> 1: NA
#> 2: NA
#> 3: NA
#> 4: NA
#> 5: NA
#> 6: NA
# Select cases by AHRQ comorbidity condition "Renal"
Case <- selectCases(dxDataFile = sampleDxFile,
idColName = ID,
icdColName = ICD,
dateColName = Date,
icd10usingDate = "2015/10/01",
groupDataType = ahrq,
isDescription = FALSE,
caseCondition = "Renal",
caseCount = 1,
periodRange = c(30, 365))
head(Case)
#> ID selectedCase count firstCaseDate endCaseDate period MostCommonICD
#> 1: A3 Selected 5 2008-07-08 2014-02-24 2057 days V420
#> 2: A1 Selected 5 2006-11-29 2014-09-24 2856 days 5855
#> 3: A10 Selected 5 2007-11-04 2012-07-30 1730 days V5631
#> 4: A12 Selected 5 2006-05-14 2015-06-29 3333 days 5859
#> 5: A13 Selected 5 2006-04-29 2025-02-02 6854 days 5855
#> 6: A15 Selected 5 2007-05-25 2023-05-12 5831 days V5631
#> MostCommonICDCount
#> 1: 3
#> 2: 2
#> 3: 2
#> 4: 2
#> 5: 2
#> 6: 2
# Select cases by CCS Level 2 condition "Diseases of the urinary system"
Case <- selectCases(dxDataFile = sampleDxFile,
idColName = ID,
icdColName = ICD,
dateColName = Date,
icd10usingDate = "2015/10/01",
groupDataType = ccslvl2,
isDescription = TRUE,
caseCondition = "Diseases of the urinary system",
caseCount = 1,
periodRange = c(30, 365))
head(Case)
#> ID selectedCase count firstCaseDate endCaseDate period MostCommonICD
#> 1: A3 Selected 5 2008-07-08 2014-02-24 2057 days V420
#> 2: A1 Selected 5 2006-11-29 2014-09-24 2856 days 5855
#> 3: A10 Selected 5 2007-11-04 2012-07-30 1730 days V5631
#> 4: A12 Selected 5 2006-05-14 2015-06-29 3333 days 5859
#> 5: A13 Selected 5 2006-04-29 2025-02-02 6854 days 5855
#> 6: A15 Selected 5 2007-05-25 2023-05-12 5831 days V5631
#> MostCommonICDCount
#> 1: 3
#> 2: 2
#> 3: 2
#> 4: 2
#> 5: 2
#> 6: 2
2. Condition era generation
# get era by the comorbidity condition ELIX
Era <- getConditionEra(dxDataFile = sampleDxFile,
idColName = ID,
icdColName = ICD,
dateColName = Date,
icd10usingDate = "2015/10/01",
groupDataType = ELIX,
isDescription = TRUE,
gapDate = 30)
head(Era)
#> ID Description era firstCaseDate endCaseDate count period
#> 1: A0 Renal failure 1 2009-07-25 2009-07-25 1 0 days
#> 2: A0 Renal failure 2 2010-03-28 2010-03-28 1 0 days
#> 3: A0 Renal failure 3 2010-10-29 2010-10-29 1 0 days
#> 4: A0 Renal failure 4 2012-04-05 2012-04-05 1 0 days
#> 5: A0 Renal failure 5 2013-12-20 2013-12-20 1 0 days
#> 6: A1 Renal failure 1 2006-11-29 2006-11-29 1 0 days
3. Analysis ready data generation
# generate analysis ready data mapped with case and Control Group
CHARLSON <- icdDxToComorbid(dxDataFile = sampleDxFile,
idColName = ID,
icdColName = ICD,
dateColName = Date,
icd10usingDate = "2015-10-01",
comorbidMethod = CHARLSON)
head(CHARLSON$groupedDT)
#> Short ID ICD Date Comorbidity
#> 1: Z992 A2 Z992 2020-05-22 RD
#> 2: Z992 A5 Z992 2020-01-24 RD
#> 3: Z992 A8 Z992 2015-10-27 RD
#> 4: Z992 A13 Z992 2020-04-26 RD
#> 5: Z992 A13 Z992 2025-02-02 RD
#> 6: Z992 A15 Z992 2023-05-12 RD
selectedCaseFile <- selectCases(dxDataFile = sampleDxFile,
idColName = ID,
icdColName = ICD,
dateColName = Date,
icd10usingDate = "2015/10/01",
groupDataType = ccs,
caseCondition = "11",
isDescription = FALSE,
caseCount = 1)
head(selectedCaseFile)
#> ID selectedCase count firstCaseDate endCaseDate period MostCommonICD
#> 1: C0 Selected 2 2016-07-05 2025-02-21 3153 days C048
#> 2: C1 Selected 1 2018-02-13 2018-02-13 0 days C320
#> 3: C2 Selected 1 2016-09-09 2016-09-09 0 days C006
#> 4: C4 Selected 1 2022-10-23 2022-10-23 0 days C130
#> 5: D4 Selected 1 2020-10-06 2020-10-06 0 days I69942
#> 6: A2 non-Selected NA <NA> <NA> NA days <NA>
#> MostCommonICDCount
#> 1: 1
#> 2: 1
#> 3: 1
#> 4: 1
#> 5: 1
#> 6: NA
groupedDataWide <- groupedDataLongToWide(dxDataFile = CHARLSON$groupedDT,
idColName = ID,
categoryColName = Comorbidity,
dateColName = Date,
reDup = TRUE,
numericOrBinary = N,
selectedCaseFile = selectedCaseFile)
tail(groupedDataWide)
#> ID CANCER CEVD COPD DIAB_C MSLD PARA PUD PVD RD Rheum selectedCase
#> 1: D3 0 0 0 0 0 0 0 1 0 0 non-Selected
#> 2: D4 1 1 0 1 0 0 0 0 0 0 Selected
#> 3: D5 1 0 1 1 0 0 0 0 0 1 non-Selected
#> 4: D6 0 0 0 0 0 0 0 0 0 0 non-Selected
#> 5: D7 1 0 0 1 0 0 0 0 0 1 non-Selected
#> 6: D8 1 0 0 0 0 1 0 1 0 0 non-Selected
III. Visualization
# Bar chart of diagnostic categories – case and control groups
selectedCaseFile <- selectCases(dxDataFile = sampleDxFile,
idColName = ID,
icdColName = ICD,
dateColName = Date,
icd10usingDate = "2015/10/01",
groupDataType = ccs,
caseCondition = "11",
isDescription = FALSE,
caseCount = 1)
groupedDataWide <- groupedDataLongToWide(dxDataFile = ELIX$groupedDT,
idColName = ID,
categoryColName = Comorbidity,
dateColName = Date,
reDup = TRUE,
numericOrBinary = B,
count = 2,
selectedCaseFile = selectedCaseFile)
plot <- plotDiagCat(groupedDataWide = groupedDataWide,
idColName = ID,
groupColName = selectedCase,
topN = 10,
limitFreq = 0.01,
pvalue = 0.05)
plot$graph
plot$sigCate
#> DiagnosticCategory Group N Percentage
#> 1: TUMOR non-Selected 1 3.03
#> 2: TUMOR Selected 4 80.00
IV. Procedure
head(samplePrFile)
#> ID ICD Date
#> 1: B 5681 2008-01-14
#> 2: A 9774 2009-01-11
#> 3: B 44.99 2009-05-10
#> 4: C 07.59 2009-01-21
#> 5: B 0205 2008-07-06
#> 6: B 8812 2007-06-27
1. Code classification
# CCS single level classification
CCS <- icdPrToCCS (prDataFile = samplePrFile,
idColName = ID,
icdColName = ICD,
dateColName = Date,
icd10usingDate = "2015-10-01",
isDescription = TRUE)
head(CCS$groupedDT)
#> Short ID ICD Date CCS_CATEGORY_DESCRIPTION
#> 1: 5681 B 5681 2008-01-14 Other OR therapeutic procedures of urinary tract
#> 2: 9774 A 9774 2009-01-11 Other non-OR therapeutic procedures; female organs
#> 3: 4499 B 44.99 2009-05-10 Other OR upper GI therapeutic procedures
#> 4: 0759 C 07.59 2009-01-21 Therapeutic endocrine procedures
#> 5: 0205 B 0205 2008-07-06 Other OR therapeutic nervous system procedures
#> 6: 8812 B 8812 2007-06-27 Other diagnostic radiology and related techniques
# ICD to CCS multiple level 1
CCSlvl <- icdPrToCCSLvl(prDataFile = samplePrFile,
idColName = ID,
icdColName = ICD,
dateColName = Date,
icd10usingDate = "2015-10-01",
CCSLevel = 2,
isDescription = FALSE)
head(CCSlvl$groupedDT)
#> Short ID ICD Date CCS_LVL_2
#> 1: 5681 B 5681 2008-01-14 10.11
#> 2: 9774 A 9774 2009-01-11 12.12
#> 3: 4499 B 44.99 2009-05-10 9.26
#> 4: 0759 C 07.59 2009-01-21 2.3
#> 5: 0205 B 0205 2008-07-06 1.9
#> 6: 8812 B 8812 2007-06-27 16.37
# Procedure class
ProcedureClass <- icdPrToProcedureClass(prDataFile = samplePrFile,
idColName = ID,
icdColName = ICD,
dateColName = Date,
icd10usingDate = "2015-10-01",
isDescription = FALSE)
head(ProcedureClass$groupedDT)
#> Short ID ICD Date PROCEDURE_CLASS
#> 1: 5681 B 5681 2008-01-14 4
#> 2: 9774 A 9774 2009-01-11 2
#> 3: 4499 B 44.99 2009-05-10 4
#> 4: 0759 C 07.59 2009-01-21 4
#> 5: 0205 B 0205 2008-07-06 4
#> 6: 8812 B 8812 2007-06-27 1
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