Nothing
## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(echo = TRUE, eval=TRUE,
fig.height=4, fig.width=6, fig.pos="ht!")
library(sequoia)
## ----RunPedComp---------------------------------------------------------------
library(sequoia)
data(SeqOUT_griffin, FieldMums_griffin, package="sequoia")
PCG <- PedCompare(Ped1 = cbind(FieldMums_griffin,
sire = NA),
Ped2 = SeqOUT_griffin$Pedigree,
SNPd = SeqOUT_griffin$PedigreePar$id,
Symmetrical = TRUE, Plot=FALSE)
## ----MergedPed----------------------------------------------------------------
PCG$MergedPed[c(127:133), c("id", "dam.1", "dam.2", "dam.class")]
## ----id-idr-sep---------------------------------------------------------------
# subset some individuals:
these <- c("i177_2009_M", "i179_2009_M", "i165_2009_F", "i166_2009_F", "F0002",
"F0007", "YellowPink", "PinkBlue")
knitr::kable(list(Ped1 = FieldMums_griffin[FieldMums_griffin$id %in% these, ],
Ped2 = SeqOUT_griffin$Pedigree[SeqOUT_griffin$Pedigree$id %in% these, 1:3]),
caption = "Subsets of Pedigree1 (left) and Pedigree2 (right)")
## ----id-idr-------------------------------------------------------------------
PCG$MergedPed[PCG$MergedPed$id %in% these,
c("id", "id.r", "dam.1", "dam.2", "dam.r")]
## ----DumMatch-----------------------------------------------------------------
head(PCG$DummyMatch[, -c(3:5)], n=6)
## ----Counts-plot--------------------------------------------------------------
PlotPedComp(PCG$Counts)
## ----Counts-------------------------------------------------------------------
PCG$Counts[,,"dam"]
## ----Mismatch1----------------------------------------------------------------
PCG$MergedPed[which(PCG$MergedPed$dam.class == "Mismatch"), c("id", "dam.1", "dam.2", "id.dam.cat")]
## ----MisMatch1----------------------------------------------------------------
PedM <- PCG$MergedPed[, c("id", "dam.1", "dam.2")] # short-hand to minimise typing
# does the mismatch affect all of GreenBlue's offspring?
PedM[which(PedM$dam.1 == "GreenBlue"), ]
# > yes, these 4 are all of her known offspring
# does genetic mother i081_2005_F have any field-observed offspring?
PedM[which(PedM$dam.1 == "i081_2005_F"), ]
# no.
# does i081_2005_F have any other genetic offspring?
PedM[which(PedM$dam.2 == "i081_2005_F"), ]
# no.
## ----MisMatch2----------------------------------------------------------------
# why is this flagged as a mismatch?
PedM[which(PedM$dam.1 == "OrangeGreen"), ]
# all of OrangeGreen's offspring are in sibship F0001
PedM[which(PedM$dam.2 == "F0001"), c("id", "dam.1", "dam.2")]
# but sibship F0001 is split across two field mothers
## ----MisMatch3----------------------------------------------------------------
# as before
PedM[which(PedM$dam.1 == "YellowBlue"), ]
# something odd going on involving sibships F0003 & F0005
PedM[which(PedM$dam.2 %in% c("F0003", "F0005")), ]
## ----Ped1only-----------------------------------------------------------------
PCG$MergedPed[which(PCG$MergedPed$dam.class == "P1only"),
c("id", "id.r", "dam.1", "dam.2", "id.dam.cat")]
## -----------------------------------------------------------------------------
SeqOUT_griffin$DummyIDs[c(6,7), c("id", "dam", "BY.est", "NumOff", "O1", "O2", "O3", "O4")]
## -----------------------------------------------------------------------------
PedX <- SeqOUT_griffin$Pedigree
# INSTEAD, SOMETHING LIKE THIS:
Name_match <- matrix(c(PedX$dam[PedX$id=='i123_2007_F'], 'OrangeGreen',
PedX$dam[PedX$id=='i165_2009_F'], 'PinkBlue',
PedX$dam[PedX$id=='i121_2007_M'], 'GreenYellow'),
ncol = 2, byrow=TRUE)
Name_match
for (i in 1:nrow(Name_match)) {
PedX$id[ PedX$id == Name_match[i,1] ] <- Name_match[i,2]
PedX$dam[ PedX$dam == Name_match[i,1] ] <- Name_match[i,2]
}
## -----------------------------------------------------------------------------
head(SeqOUT_griffin$DummyIDs[, c('id','dam','sire','NumOff','O1','O2','O3')])
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