I am trying to find out the genes with expression level correlated to the trait (coded as 0 and 1) with phylolm. I have one question.
When I run the phylolm using following command:
library('ape')
library('phylolm')
setwd("path)
getwd()
samples = read.table("expression_trait_file",row.names=1)
tree = read.nexus("tree", tree.names = NULL, force.multi = FALSE)
fit = phyloglm(formula=pigment~tpm, data=samples, phy=tree, method = ("logistic_MPLE"), boot = 0)
summary(fit)
coef(fit)
vcov(fit)
Could you kindly me let me know how I can know if the gene expression is significantly correlated to the trait (coded a 0 and 1) from the output? In other words, could you kindly tell me how to explain the results?
Thank you very much.
Hello,
I am trying to find out the genes with expression level correlated to the trait (coded as 0 and 1) with phylolm. I have one question. When I run the phylolm using following command: library('ape') library('phylolm') setwd("path) getwd() samples = read.table("expression_trait_file",row.names=1) tree = read.nexus("tree", tree.names = NULL, force.multi = FALSE) fit = phyloglm(formula=pigment~tpm, data=samples, phy=tree, method = ("logistic_MPLE"), boot = 0) summary(fit) coef(fit) vcov(fit)
I got results as following:
Call: phyloglm(formula = pigment ~ tpm, data = samples, phy = tree, method = ("logistic_MPLE"), boot = 0) AIC logLik Pen.logLik 44.35 -19.17 -16.78
Method: logistic_MPLE Mean tip height: 0.3558203 Parameter estimate(s): alpha: 2.787424
Coefficients: Estimate StdErr z.value p.value
(Intercept) -2.091304 1.114385 -1.8766 0.06057 . tpm 0.142301 0.099049 1.4367 0.15081
Signif. codes: 0 ‘’ 0.001 ‘’ 0.01 ‘’ 0.05 ‘.’ 0.1 ‘ ’ 1
Note: Wald-type p-values for coefficients, conditional on alpha=2.787424
Could you kindly me let me know how I can know if the gene expression is significantly correlated to the trait (coded a 0 and 1) from the output? In other words, could you kindly tell me how to explain the results? Thank you very much.
Best regards,
Lingyun