Commit 83392b9f authored by Holger Brandl's avatar Holger Brandl

added autolabeling to intersectin utils

parent 23e3dd6b
......@@ -107,31 +107,40 @@ getGeneInfo <- function(gene_ids){
extractHits <- function(deData, s1, s2, s1Overexpressed=T){
# note one of the two sets will always be empty; Example: s1="small_cyst"; s2="liver_polar_stage1"
forward <- subset(deData, sample_1==s1 & sample_2==s2 & sample_1_overex==s1Overexpressed)$ensembl_gene_id %>% ac()
reverse <- subset(deData, sample_1==s2 & sample_2==s1 & sample_1_overex==!s1Overexpressed)$ensembl_gene_id %>% ac()
forward <- subset(deData, sample_1==s1 & sample_2==s2 & sample_1_overex==s1Overexpressed) %$% ac(gene_id)
reverse <- subset(deData, sample_1==s2 & sample_2==s1 & sample_1_overex==!s1Overexpressed) %$% ac(gene_id)
return(c(forward, reverse))
}
## genes that are significantly higher expressed in sample1 compared to sample2
s1_gt_s2 <- function(deData, s1, s2) extractHits(deData, s1, s2, s1Overexpressed=T)
s1_gt_s2 <- function(deData, sample_1, sample_2){
extractHits(deData, sample_1, sample_2, s1Overexpressed=T) %>%
data_frame(gene_id=., list_id = paste(sample_1, ">", sample_2))
}
## genes that are significantly less expressed in sample1 compared to sample2
s1_lt_s2 <- function(deData, s1, s2) extractHits(deData, s1, s2, s1Overexpressed=F)
s1_lt_s2 <- function(deData, sample_1, sample_2){
extractHits(deData, sample_1, sample_2, s1Overexpressed=F) %>%
data_frame(gene_id=., list_id = paste(sample_1, "<", sample_2))
}
## undirected, just differentially expressed
s1_de_s2 <- function(deData, s1, s2){
c(extractHits(deData, s1, s2, s1Overexpressed=F), extractHits(deData, s1, s2, s1Overexpressed=T));
s1_de_s2 <- function(deData, sample_1, sample_2){
c(extractHits(deData, sample_1, s2, s1Overexpressed=F), extractHits(deData, s1, sample_2, s1Overexpressed=T)) %>%
data_frame(gene_id=., list_id = paste(sample_1, "!=", sample_2))
}
## not differentially expressed
s1_eq_s2 <- function(deData, s1, s2, gene_background=all_genes){
s1_eq_s2 <- function(deData, sample_1, sample_2, gene_background=all_genes){
c(
extractHits(deData, s1, s2, s1Overexpressed=F, ...),
extractHits(deData, s1, s2, s1Overexpressed=T, ...)
extractHits(deData, sample_1, sample_2, s1Overexpressed=F, ...),
extractHits(deData, sample_1, sample_2, s1Overexpressed=T, ...)
) %>%
setdiff(all_genes, .)
setdiff(gene_background, .) %>%
mutate(list_id = paste(sample_1, "==", sample_2))
}
......@@ -140,10 +149,11 @@ diff_intersect <- function(deData, sample_1, sample_twoes, .intersect_method, ..
# rec_intersect sample_twoes = list(...)
# sample_twoes <- list(); sample_1="VZ"
rec_intersect <- .intersect_method(deData, sample_1, sample_twoes[1], ...)
#browser()
rec_intersect <- .intersect_method(deData, sample_1, sample_twoes[1], ...)$gene_id
for (i in 2:length(sample_twoes)) {
rec_intersect <- intersect(rec_intersect, .intersect_method(deData, sample_1, sample_twoes[i], ...))
rec_intersect <- intersect(rec_intersect, .intersect_method(deData, sample_1, sample_twoes[i], ...)$gene_id)
}
......
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