Dear R users,
I am running the following code below, the gem751be.rpkm is a dataframe with
dim of 751 samples by 35164 variables, 73 phenotypic variables in the furst to
73rd column and 35091 genomic variables or genes in the 74th to 35164th
columns. What I need to do is to calculate the residuals for each gene using
the simple linear regression model of genelist[i] ~ purity2;
The following code is running, it takes long time, but I have an expensive
ThinkStation window computer.
Can you provide a fast way to do it?
Thank you,
Ding
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gem751be.rpkm <-merge(gem751be10, as.data.frame(t(rna849.fpkm2)),
+ by.x="id2",by.y=0)
> row.names(gem751be.rpkm)<-gem751be.rpkm$id3
>
> colnames(gem751be.rpkm)<-gsub(colnames(gem751be.rpkm),pattern="-",replacement="_")
> genelist <- gem751be.rpkm %>% dplyr::select(74:35164)
> residuals <- NULL
> for (i in 1:length(genelist)) {
+ #i=1
+ formula <- reformulate("purity2", response=names(genelist)[i])
+ model <- lm(formula, data = gem751be.rpkm)
+ resi <- as.data.frame(residuals(model))
+ colnames(resi)[1]<-names(genelist)[i]
+ resi <-as.data.frame(t(resi))
+ residuals <- rbind(residuals, resi)
+ }
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