Last updated: 2021-06-10
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Knit directory: implementGMSinCassava/
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Follow outlined GenomicPredictionChecklist and previous pipeline to process cassavabase data for ultimate genomic prediction.
Below we will clean and format training data.
Downloaded all IITA field trials.
Selected all IITA trials currently available. Make a list. Named it ALL_IITA_TRIALS_2021May04.
Go to Manage –> Download here. Download phenotypes (plot-basis only) and meta-data as CSV using the corresponding boxes / drop-downs.
Store flatfiles, unaltered in directory data/DatabaseDownload_2021May04/.
rm(list=ls())
library(tidyverse); library(magrittr);
source(here::here("code","gsFunctions.R"))Read DB data.
dbdata<-readDBdata(phenotypeFile = here::here("data/DatabaseDownload_2021May04"
,"2021-05-04T193557phenotype_download.csv"),
metadataFile = here::here("data/DatabaseDownload_2021May04"
,"2021-05-04T194847metadata_download.csv"))Make TrialType Variable
dbdata<-makeTrialTypeVar(dbdata)
dbdata %>%
count(TrialType) %>% rmarkdown::paged_table()Looking at the studyName’s of trials getting NA for TrialType, which can’t be classified at present.
Here is the list of trials I am not including.
dbdata %>% filter(is.na(TrialType)) %$% unique(studyName) %>%
write.csv(.,file = here::here("output","IITA_trials_NOT_identifiable.csv"), row.names = F)Wrote to disk a CSV in the output/ sub-directory.
Should any of these trials have been included?
Especially among the following new trials (post 2018):
dbdata %>%
filter(is.na(TrialType),
as.numeric(studyYear)>2018) %$% unique(studyName)dbdata %<>%
filter(!is.na(TrialType))
dbdata %>%
group_by(programName) %>%
summarize(N=n()) %>% rmarkdown::paged_table()
# May 2021: 524390 (now including a ~200K plot seedling nursery) plots
## Dec 2020: 475097 plots (~155K are seedling nurseries which will be excluded from most analyses)Making a table of abbreviations for renaming. Since July 2019 version: added chromometer traits (L, a, b) and added branching levels count (BRLVLS) at IYR’s request.
traitabbrevs<-tribble(~TraitAbbrev,~TraitName,
"CMD1S","cassava.mosaic.disease.severity.1.month.evaluation.CO_334.0000191",
"CMD3S","cassava.mosaic.disease.severity.3.month.evaluation.CO_334.0000192",
"CMD6S","cassava.mosaic.disease.severity.6.month.evaluation.CO_334.0000194",
"CMD9S","cassava.mosaic.disease.severity.9.month.evaluation.CO_334.0000193",
"CGM","Cassava.green.mite.severity.CO_334.0000033",
"CGMS1","cassava.green.mite.severity.first.evaluation.CO_334.0000189",
"CGMS2","cassava.green.mite.severity.second.evaluation.CO_334.0000190",
"DM","dry.matter.content.percentage.CO_334.0000092",
"PLTHT","plant.height.measurement.in.cm.CO_334.0000018",
"BRNHT1","first.apical.branch.height.measurement.in.cm.CO_334.0000106",
"BRLVLS","branching.level.counting.CO_334.0000079",
"SHTWT","fresh.shoot.weight.measurement.in.kg.per.plot.CO_334.0000016",
"RTWT","fresh.storage.root.weight.per.plot.CO_334.0000012",
"RTNO","root.number.counting.CO_334.0000011",
"TCHART","total.carotenoid.by.chart.1.8.CO_334.0000161",
"LCHROMO","L.chromometer.value.CO_334.0002065",
"ACHROMO","a.chromometer.value.CO_334.0002066",
"BCHROMO","b.chromometer.value.CO_334.0002064",
"NOHAV","plant.stands.harvested.counting.CO_334.0000010")
traitabbrevs %>% rmarkdown::paged_table()Run function renameAndSelectCols() to rename columns and remove everything unecessary
dbdata<-renameAndSelectCols(traitabbrevs,indata=dbdata,customColsToKeep = c("TrialType","observationUnitName"))dbdata<-dbdata %>%
mutate(CMD1S=ifelse(CMD1S<1 | CMD1S>5,NA,CMD1S),
CMD3S=ifelse(CMD3S<1 | CMD3S>5,NA,CMD3S),
CMD6S=ifelse(CMD6S<1 | CMD6S>5,NA,CMD6S),
CMD9S=ifelse(CMD9S<1 | CMD9S>5,NA,CMD9S),
CGM=ifelse(CGM<1 | CGM>5,NA,CGM),
CGMS1=ifelse(CGMS1<1 | CGMS1>5,NA,CGMS1),
CGMS2=ifelse(CGMS2<1 | CGMS2>5,NA,CGMS2),
DM=ifelse(DM>100 | DM<=0,NA,DM),
RTWT=ifelse(RTWT==0 | NOHAV==0 | is.na(NOHAV),NA,RTWT),
SHTWT=ifelse(SHTWT==0 | NOHAV==0 | is.na(NOHAV),NA,SHTWT),
RTNO=ifelse(RTNO==0 | NOHAV==0 | is.na(NOHAV),NA,RTNO),
NOHAV=ifelse(NOHAV==0,NA,NOHAV),
NOHAV=ifelse(NOHAV>42,NA,NOHAV),
RTNO=ifelse(!RTNO %in% 1:10000,NA,RTNO))dbdata<-dbdata %>%
mutate(HI=RTWT/(RTWT+SHTWT))I anticipate this will not be necessary as it will be computed before or during data upload.
For calculating fresh root yield:
dbdata<-dbdata %>%
mutate(PlotSpacing=ifelse(programName!="IITA",1,
ifelse(studyYear<2013,1,
ifelse(TrialType %in% c("CET","GeneticGain","ExpCET"),1,0.8))))
maxNOHAV_byStudy<-dbdata %>%
group_by(programName,locationName,studyYear,studyName,studyDesign) %>%
summarize(MaxNOHAV=max(NOHAV, na.rm=T)) %>%
ungroup() %>%
mutate(MaxNOHAV=ifelse(MaxNOHAV=="-Inf",NA,MaxNOHAV))
write.csv(maxNOHAV_byStudy %>% arrange(studyYear),file=here::here("output","maxNOHAV_byStudy.csv"), row.names = F)# I log transform yield traits
# to satisfy homoskedastic residuals assumption
# of linear mixed models
dbdata<-left_join(dbdata,maxNOHAV_byStudy) %>%
mutate(RTWT=ifelse(NOHAV>MaxNOHAV,NA,RTWT),
SHTWT=ifelse(NOHAV>MaxNOHAV,NA,SHTWT),
RTNO=ifelse(NOHAV>MaxNOHAV,NA,RTNO),
HI=ifelse(NOHAV>MaxNOHAV,NA,HI),
FYLD=RTWT/(MaxNOHAV*PlotSpacing)*10,
DYLD=FYLD*(DM/100),
logFYLD=log(FYLD),
logDYLD=log(DYLD),
logTOPYLD=log(SHTWT/(MaxNOHAV*PlotSpacing)*10),
logRTNO=log(RTNO),
PropNOHAV=NOHAV/MaxNOHAV)
# remove non transformed / per-plot (instead of per area) traits
dbdata %<>% select(-RTWT,-SHTWT,-RTNO,-FYLD,-DYLD)# [NEW AS OF APRIL 2021]
## VERSION with vs. without CBSD
## Impervious to particular timepoints between 1, 3, 6 and 9 scores
# Without CBSD (West Africa)
dbdata<-dbdata %>%
mutate(MCMDS=rowMeans(.[,colnames(.) %in% c("CMD1S","CMD3S","CMD6S","CMD9S")], na.rm = T)) %>%
select(-any_of(c("CMD1S","CMD3S","CMD6S","CMD9S")))
# With CBSD (East Africa)
# dbdata<-dbdata %>%
# mutate(MCMDS=rowMeans(.[,colnames(.) %in% c("CMD1S","CMD3S","CMD6S","CMD9S")], na.rm = T),
# MCBSDS=rowMeans(.[,colnames(.) %in% c("CBSD1S","CBSD3S","CBSD6S","CBSD9S")], na.rm = T)) %>%
# select(-any_of(c("CMD1S","CMD3S","CMD6S","CMD9S","CBSD1S","CBSD3S","CBSD6S","CBSD9S")))This step is mostly copy-pasted from previous processing of IITA- and IITA-specific data.
Uses 4 flat files, which are available e.g. here. Specifically, IITA_GBStoPhenoMaster_33018.csv, GBSdataMasterList_31818.csv and IITA_GBStoPhenoMaster_40318.csv and chr1_RefPanelAndGSprogeny_ReadyForGP_72719.fam. I copy them to the data/ sub-directory for the current analysis.
In addition, DArT-only samples are now expected to also have phenotypes. Therefore, checking for matches in new flatfiles, deposited in the data/ (see code below).
library(tidyverse); library(magrittr)
gbs2phenoMaster<-dbdata %>%
select(germplasmName) %>%
distinct %>%
left_join(read.csv(here::here("data","NRCRI_GBStoPhenoMaster_40318.csv"),
stringsAsFactors = F)) %>%
mutate(FullSampleName=ifelse(grepl("C2a",germplasmName,ignore.case = T) &
is.na(FullSampleName),germplasmName,FullSampleName)) %>%
filter(!is.na(FullSampleName)) %>%
select(germplasmName,FullSampleName) %>%
bind_rows(dbdata %>%
select(germplasmName) %>%
distinct %>%
left_join(read.csv(here::here("data","IITA_GBStoPhenoMaster_33018.csv"),
stringsAsFactors = F)) %>%
filter(!is.na(FullSampleName)) %>%
select(germplasmName,FullSampleName)) %>%
bind_rows(dbdata %>%
select(germplasmName) %>%
distinct %>%
left_join(read.csv(here::here("data","GBSdataMasterList_31818.csv"),
stringsAsFactors = F) %>%
select(DNASample,FullSampleName) %>%
rename(germplasmName=DNASample)) %>%
filter(!is.na(FullSampleName)) %>%
select(germplasmName,FullSampleName)) %>%
bind_rows(dbdata %>%
select(germplasmName) %>%
distinct %>%
mutate(germplasmSynonyms=ifelse(grepl("^UG",germplasmName,ignore.case = T),
gsub("UG","Ug",germplasmName),germplasmName)) %>%
left_join(read.csv(here::here("data","GBSdataMasterList_31818.csv"),
stringsAsFactors = F) %>%
select(DNASample,FullSampleName) %>%
rename(germplasmSynonyms=DNASample)) %>%
filter(!is.na(FullSampleName)) %>%
select(germplasmName,FullSampleName)) %>%
bind_rows(dbdata %>%
select(germplasmName) %>%
distinct %>%
mutate(germplasmSynonyms=ifelse(grepl("^TZ",germplasmName,
ignore.case = T),
gsub("TZ","",germplasmName),germplasmName)) %>%
left_join(read.csv(here::here("data","GBSdataMasterList_31818.csv"),
stringsAsFactors = F) %>%
select(DNASample,FullSampleName) %>%
rename(germplasmSynonyms=DNASample)) %>%
filter(!is.na(FullSampleName)) %>%
select(germplasmName,FullSampleName)) %>%
distinct %>%
left_join(read.csv(here::here("data","GBSdataMasterList_31818.csv"),
stringsAsFactors = F) %>%
select(FullSampleName,OrigKeyFile,Institute) %>%
rename(OriginOfSample=Institute)) %>%
mutate(OrigKeyFile=ifelse(grepl("C2a",germplasmName,ignore.case = T),
ifelse(is.na(OrigKeyFile),"LavalGBS",OrigKeyFile),
OrigKeyFile),
OriginOfSample=ifelse(grepl("C2a",germplasmName,ignore.case = T),
ifelse(is.na(OriginOfSample),"NRCRI",OriginOfSample),
OriginOfSample))
## NEW: check for germName-DArT name matches
germNamesWithoutGBSgenos<-dbdata %>%
select(programName,germplasmName) %>%
distinct %>%
left_join(gbs2phenoMaster) %>%
filter(is.na(FullSampleName)) %>%
select(-FullSampleName)
## NEW: check for germName-DArT name matches
germNamesWithoutGBSgenos<-dbdata %>%
select(programName,germplasmName) %>%
distinct %>%
left_join(gbs2phenoMaster) %>%
filter(is.na(FullSampleName)) %>%
select(-FullSampleName)
germNamesWithDArT<-germNamesWithoutGBSgenos %>%
inner_join(read.table(here::here("data","chr1_RefPanelAndGSprogeny_ReadyForGP_72719.fam"),
header = F, stringsAsFactors = F)$V2 %>%
grep("TMS16|TMS17|TMS18|TMS19|TMS20",.,value = T, ignore.case = T) %>%
tibble(dartName=.) %>%
separate(dartName,c("germplasmName","dartID"),"_",extra = 'merge',remove = F)) %>%
group_by(germplasmName) %>%
slice(1) %>%
ungroup() %>%
rename(FullSampleName=dartName) %>%
mutate(OrigKeyFile="DArTseqLD", OriginOfSample="IITA") %>%
select(-dartID)
print(paste0(nrow(germNamesWithDArT)," germNames with DArT-only genos"))
# first, filter to just program-DNAorigin matches
germNamesWithGenos<-dbdata %>%
select(programName,germplasmName) %>%
distinct %>%
left_join(gbs2phenoMaster) %>%
filter(!is.na(FullSampleName))
print(paste0(nrow(germNamesWithGenos)," germNames with GBS genos"))
# program-germNames with locally sourced GBS samples
germNamesWithGenos_HasLocalSourcedGBS<-germNamesWithGenos %>%
filter(programName==OriginOfSample) %>%
select(programName,germplasmName) %>%
semi_join(germNamesWithGenos,.) %>%
group_by(programName,germplasmName) %>% # select one DNA per germplasmName per program
slice(1) %>% ungroup()
print(paste0(nrow(germNamesWithGenos_HasLocalSourcedGBS)," germNames with local GBS genos"))
# the rest (program-germNames) with GBS but coming from a different breeding program
germNamesWithGenos_NoLocalSourcedGBS<-germNamesWithGenos %>%
filter(programName==OriginOfSample) %>%
select(programName,germplasmName) %>%
anti_join(germNamesWithGenos,.) %>%
# select one DNA per germplasmName per program
group_by(programName,germplasmName) %>%
slice(1) %>% ungroup()
print(paste0(nrow(germNamesWithGenos_NoLocalSourcedGBS)," germNames without local GBS genos"))
genosForPhenos<-bind_rows(germNamesWithGenos_HasLocalSourcedGBS,
germNamesWithGenos_NoLocalSourcedGBS) %>%
bind_rows(germNamesWithDArT)
print(paste0(nrow(genosForPhenos)," total germNames with genos either GBS or DArT"))
dbdata %<>%
left_join(genosForPhenos)
# Create a new identifier, GID
## Equals the value SNP data name (FullSampleName)
## else germplasmName if no SNP data
dbdata %<>%
mutate(GID=ifelse(is.na(FullSampleName),germplasmName,FullSampleName))# # going to check against SNP data
# snps<-readRDS(file=url(paste0("ftp://ftp.cassavabase.org/marnin_datasets/NGC_BigData/",
# "DosageMatrix_RefPanelAndGSprogeny_ReadyForGP_73019.rds")))
# rownames_snps<-rownames(snps); rm(snps); gc()
# # current matches to SNP data
# dbdata %>%
# distinct(GID,germplasmName,FullSampleName) %>%
# semi_join(tibble(GID=rownames_snps)) %>% nrow() # 10707
# dbdata %>%
# distinct(GID,germplasmName,FullSampleName) %>%
# semi_join(tibble(GID=rownames_snps)) %>%
# filter(grepl("TMS13|2013_",GID,ignore.case = F)) %>% nrow() # 2424 TMS13
# dbdata %>%
# distinct(GID,germplasmName,FullSampleName) %>%
# semi_join(tibble(GID=rownames_snps)) %>%
# filter(grepl("TMS14",GID,ignore.case = F)) %>% nrow() # 2236 TMS14
# dbdata %>%
# distinct(GID,germplasmName,FullSampleName) %>%
# semi_join(tibble(GID=rownames_snps)) %>%
# filter(grepl("TMS15",GID,ignore.case = F)) %>% nrow() # 2287 TMS15
# dbdata %>%
# distinct(GID,germplasmName,FullSampleName) %>%
# semi_join(tibble(GID=rownames_snps)) %>%
# filter(grepl("TMS18",GID,ignore.case = F)) %>% nrow() # 2401 TMS18WARNING: User input required! If I had preselected locations before downloading, this wouldn’t have been necessary.
Based on previous locations used for IITA analysis, but adding based on list of locations used in IYR’s trial list data/2019_GS_PhenoUpload.csv: “Ago-Owu” wasn’t used last year.
dbdata %<>%
filter(locationName %in% c("Abuja","Ago-Owu","Ibadan","Ikenne","Ilorin","Jos","Kano",
"Malam Madori","Mokwa","Ubiaja","Umudike","Warri","Zaria"))
nrow(dbdata) # [1] 479588saveRDS(dbdata,file=here::here("output","IITA_CleanedTrialData_2021May10.rds"))The next step is to check the experimental design of each trial. If you are absolutely certain of the usage of the design variables in your dataset, you might not need this step.
Examples of reasons to do the step below:
One reason it might be important to get this right is that the variance among complete blocks might not be the same among incomplete blocks. If we treat a mixture of complete and incomplete blocks as part of the same random-effect (replicated-within-trial), we assume they have the same variance.
Also error variances might be heterogeneous among different trial-types (blocking scheme available) and/or plot sizes (maxNOHAV).
Start with cleaned data from previous step.
rm(list=ls()); gc()
library(tidyverse); library(magrittr);
source(here::here("code","gsFunctions.R"))
dbdata<-readRDS(here::here("output","IITA_CleanedTrialData_2021May10.rds"))dbdata %>% head %>% rmarkdown::paged_table()Detect designs
dbdata<-detectExptDesigns(dbdata)dbdata %>%
count(programName,CompleteBlocks,IncompleteBlocks) %>% rmarkdown::paged_table()saveRDS(dbdata,file=here::here("output","IITA_ExptDesignsDetected_2021May10.rds"))
sessionInfo()