library(dsQTL)
data(DSQ_2)
DSQ_2
rd = assays(DSQ_2)[[1]]
rd
normDHS = assays(DSQ_2)[[1]]
DSQ_2
par(mfrow=c(4,1))
ranges(DSQ_2)
getClass(class(DSQ_2))
rd = rowData(DSQ_2)
plot(start(rd), ad[,1])
plot(start(rd), normDHS[,1])
plot(start(rd), normDHS[,2])
plot(start(rd)[1:4000], normDHS[1:4000,2])
plot(start(rd)[1:4000], normDHS[1:1000,2])
plot(start(rd)[1:1000], normDHS[1:1000,2])
plot(start(rd)[1:100], normDHS[1:100,2])
plot(start(rd)[1:100], abs(normDHS[1:100,2]))
plot(start(rd)[1:100], exp(normDHS[1:100,2]))
plot(start(rd)[1:100], exp(normDHS[1:100,3]))
plot(start(rd)[1:100], exp(normDHS[1:100,4]))
plot(start(rd)[1:100], exp(normDHS[1:100,5]))
plot(start(rd)[1000:1100], exp(normDHS[1000:1100,5]))
plot(start(rd)[1000:1100], exp(normDHS[1000:1100,6]))
plot(start(rd)[1000:1050], exp(normDHS[1000:1050,6]))
plot(start(rd)[1000:1050], exp(normDHS[1000:1050,7]))
plot(start(rd)[1000:1050], exp(normDHS[1000:1050,8]))
plot(start(rd)[1000:1050], exp(normDHS[1000:1050,8]))
plot(start(rd)[1000:1050], exp(normDHS[1000:1050,9]))
objects()
data(package="dsQTL")
data(meanGT_chr2)
meanGT_chr2[1:5,1:5]
grep("455173", as.character(meanGT_chr2$snpid), value=TRUE)
grep("\\.4551....", as.character(meanGT_chr2$snpid), value=TRUE)
rsid = as.character(meanGT_chr2$snpid)
rsid[1:5]
rownames(meanGT_chr2) = rsid
objects()
normDHS[1:5,1:4]
dim(normDHS)
CN = colnames(normDHS)
meanGT_chr2b = meanGT_chr2[, CN]
dim(meanGT_chr2b)
meanGT_chr2b[1:5,1:10]
meanGT_chr2 = meanGT_chr2b
save(meanGT_chr2, file="meanGT_chr2.rda")
grep("\\.4551....", rownames(meanGT_chr2), value=TRUE)
rd
targ = GRanges("chr2", IRanges(45517342,width=1))
targ
nearest(targ, ranges(rd))
nearest(ranges(targ), ranges(rd))
par(mfrow=c(3,3))
plot(normDHS[23860,]~ meanGT_chr2["chr2.45517127",])
class(meanGT_chr2)
meanGT_chr2 = data.matrix(meanGT_chr2)
plot(normDHS[23860,]~ meanGT_chr2["chr2.45517127",])
which(rownames(meanGT_chr2)== "chr2.45517127")
meanGT_chr2[285653:285660,1:5]
meanGT_chr2[285650:285680,1:5]
plot(normDHS[23860,]~ meanGT_chr2["chr2.45517549",])
plot(exp(normDHS[23860,])~ meanGT_chr2["chr2.45517549",])
plot(exp(normDHS[23860,])~ meanGT_chr2["chr2.45517770",])
plot(normDHS[23859,]~ meanGT_chr2["chr2.45517549",])
plot(normDHS[23861,]~ meanGT_chr2["chr2.45517549",])
plot(normDHS[23862,]~ meanGT_chr2["chr2.45517549",])
plot(normDHS[23863,]~ meanGT_chr2["chr2.45517549",])
y2 = getSS
library(GGdata)
y2s = colnames(smList(y2)[[1]])
y2 = getSS
y2 = getSS("hmyriB36", "2")
y2s = colnames(smList(y2)[[1]])
y2gt = as(smList(y2)[[1]], "character")
table(y2gt[,"rs4953223"])
colnames(y2gt) = y2s
rownames(y2gt) = sampleNames(y2)
table(y2gt[,"rs4953223"])
y2gt[1:5,1:5]
save(y2gt, file="y2gt.rda")
objects()
meanGT_chr2["chr2.45370846",]
table(.Last.value)
class(meanGT_chr2)
save(meanGT_chr2, file="meanGT_chr2.rda")
nearest(ranges(targ), ranges(rd))
targ
ranges(targ) = IRanges(45370800,width=1)
nearest(ranges(targ), ranges(rd))
plot(normDHS[23829,]~ meanGT_chr2["chr2.45370846",])
plot(normDHS[23829,]~ factor(round(meanGT_chr2["chr2.45370846",],0))
)
savehistory(file="foundit.hist.txt")
