how to make a vector of different values in R - r

Question

I have a matrix (data1) looking like:
gene S869 S907 S909 S016 S090 S160
1 S1 0 0 0 0.000000 0 0
2 S2 0 0 0 0.000000 0 0
3 S3 0 0 0 0.423405 0 0
4 S4 0 0 0 0.000000 0 0
5 S5 0 0 0 0.000000 0 0
6 S6 0 0 0 0.000000 0 0
I want to make a vector (Say X) for this matrix. I have another dataset (data2) looking like:
Cultivar Dose
S869 10
S907 5
S909 7
S016 19
S090 15
S160 12
Then I want to do a linear regression using
for (gene in 1:ngenes){
model = lm(Dose~X[gene,])
}
and also want to get the p values from above regression. Thank you in advance!

Answer 1

If we want to use the 'Cultivar' to extract the column names, loop over the 'Cultivar', 'Dose' corresponding values with Map, extract the column based on the 'Culivar' value for 'data1', create a new column 'Dose' with transform and apply the lm, extract the p values from the coefficients
lst1 <- Map(function(x, y) {
tmpdat <- transform(as.data.frame(data1)[x], Dose = y)
model <- lm(Dose ~ ., data = tmpdat)
coef(summary(model))[, "Pr(>|t|)"]}, data2$Cultivar, data2$Dose)
lst1
#$S869
#[1] 1.218223e-78
#$S907
#[1] 1.218223e-78
#$S909
#[1] 2.265096e-79
#...
data
data1 <- structure(list(gene = c("S1", "S2", "S3", "S4", "S5", "S6"),
S869 = c(0L, 0L, 0L, 0L, 0L, 0L), S907 = c(0L, 0L, 0L, 0L,
0L, 0L), S909 = c(0L, 0L, 0L, 0L, 0L, 0L), S016 = c(0, 0,
0.423405, 0, 0, 0), S090 = c(0L, 0L, 0L, 0L, 0L, 0L), S160 = c(0L,
0L, 0L, 0L, 0L, 0L)), class = "data.frame", row.names = c("1",
"2", "3", "4", "5", "6"))
data2 <- structure(list(Cultivar = c("S869", "S907", "S909", "S016", "S090",
"S160"), Dose = c(10L, 5L, 7L, 19L, 15L, 12L)), class = "data.frame",
row.names = c(NA,
-6L))