polarolouis/anova-phylogenetique-projet-msv
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Louis Lacoste 2024-02-21 16:13:49 +01:00
parent c87e981fef
commit 6ef1bed74f
1 changed files with 13 additions and 21 deletions
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34
R/realTreeMethod.R
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@ -37,9 +37,11 @@ data.norm <- data.norm * 1e6
data.trans <- log2(data.norm)
rownames(data.trans) <- rownames(compcodeR:::count.matrix(cdata))
# computing pvalues vec for all genes
pvalue_vec_vanilla <- sapply(seq(1,nrow(data.trans)), function(row_id) {
trait <- data.trans[row_id,]
### Pvalues computation
#  computing pvalues vec for all genes
pvalue_vec_vanilla <- sapply(seq(1, nrow(data.trans)), function(row_id) {
trait <- data.trans[row_id, ]
fit_phylo <- phylolm(trait ~ design_data$condition, phy = cdata@tree, measurement_error = TRUE)
compute_vanilla_pvalue(fit_phylo)
})
@ -48,8 +50,8 @@ pvalue_vec_vanilla <- setNames(pvalue_vec_vanilla, rownames(data.trans))
pvalue_vec_vanilla_adj <- p.adjust(pvalue_vec_vanilla, method = "BH")
pvalue_vec_satterthwaite <- sapply(seq(1,nrow(data.trans)), function(row_id) {
trait <- data.trans[row_id,]
pvalue_vec_satterthwaite <- sapply(seq(1, nrow(data.trans)), function(row_id) {
trait <- data.trans[row_id, ]
fit_phylo <- phylolm(trait ~ design_data$condition, phy = cdata@tree, measurement_error = TRUE)
compute_satterthwaite_pvalue(fit_phylo, tree = cdata@tree)
})
@ -59,8 +61,8 @@ pvalue_vec_satterthwaite <- setNames(pvalue_vec_satterthwaite, rownames(data.tra
pvalue_vec_satterthwaite_adj <- p.adjust(pvalue_vec_satterthwaite, method = "BH")
pvalue_vec_lrt <- sapply(seq(1,nrow(data.trans)), function(row_id) {
trait <- data.trans[row_id,]
pvalue_vec_lrt <- sapply(seq(1, nrow(data.trans)), function(row_id) {
trait <- data.trans[row_id, ]
fit_phylo <- phylolm(trait ~ design_data$condition, phy = cdata@tree, measurement_error = TRUE)
compute_lrt_pvalue(fit_phylo, tree = cdata@tree)
})
@ -69,25 +71,15 @@ pvalue_vec_lrt <- setNames(pvalue_vec_lrt, rownames(data.trans))
pvalue_vec_lrt_adj <- p.adjust(pvalue_vec_lrt, method = "BH")
# REML
pvalue_vec_satterthwaite.REML <- sapply(seq(1,nrow(data.trans)), function(row_id) {
trait <- data.trans[row_id,]
pvalue_vec_satterthwaite.REML <- sapply(seq(1, nrow(data.trans)), function(row_id) {
trait <- data.trans[row_id, ]
fit_phylo <- phylolm(trait ~ design_data$condition, phy = cdata@tree, measurement_error = TRUE)
compute_satterthwaite_pvalue(fit_phylo, tree = cdata@tree, REML = TRUE)
})
pvalue_vec_satterthwaite.REML <- setNames(pvalue_vec_satterthwaite, rownames(data.trans))
pvalue_vec_satterthwaite.REML <- setNames(pvalue_vec_satterthwaite.REML, rownames(data.trans))
pvalue_vec_satterthwaite_adj.REML <- p.adjust(pvalue_vec_satterthwaite, method = "BH")
pvalue_vec_lrt <- sapply(seq(1,nrow(data.trans)), function(row_id) {
trait <- data.trans[row_id,]
fit_phylo <- phylolm(trait ~ design_data$condition, phy = cdata@tree, measurement_error = TRUE)
compute_lrt_pvalue(fit_phylo, tree = cdata@tree)
})
pvalue_vec_lrt <- setNames(pvalue_vec_lrt, rownames(data.trans))
pvalue_vec_lrt_adj <- p.adjust(pvalue_vec_lrt, method = "BH")
pvalue_vec_satterthwaite_adj.REML <- p.adjust(pvalue_vec_satterthwaite.REML, method = "BH")
# TODO Histogramme des pvalues