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jianan / qtlpvl

testing of pleiotrophy vs close linkage
http://jianan.github.io/qtlpvl
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Error in lm_resid_llt(X, Y) : could not find function "lm_resid_llt" #10

Closed plycs1994 closed 3 years ago

plycs1994 commented 3 years ago

Hello

Using R version 4.0.0 and has been tried on multiple computers. I am following the "Introduction to qtlpvl" guide - the following code runs fine:

library(qtlpvl)
data(fake.phenos)
data(listeria)
listeria <- calc.genoprob(listeria, step=1)
chr <- 1
plotLOD(Y=fake.phenos, cross=listeria, chr=chr)

However when performing the multi-trait mapping I get the following error:

out <- scanone.mvn(cross=listeria, Y=fake.phenos, chr=chr)

Error in lm_resid_llt(X, Y) : could not find function "lm_resid_llt"

I get the same error if using my own data too. It appears to come from calling the lm.resid() function within scanone.mvn and I am ignorant of how to fix this. I hope this can be resolved - thank you!!

jianan commented 3 years ago

It seems devtools install the package from HEAD by default now, while this package should be installed from master branch.

Please try reinstall the package with the following command:

devtools::install_github('jianan/qtlpvl', ref="master")
plycs1994 commented 3 years ago

Thank you - this has fixed this error