simpleCap <- function(x) {
s <- strsplit(x, " ")[[1]]
paste((substring(s, 1,1)), tolower(substring(s, 2)),
sep="", collapse=" ")
}We check here whether depletion is enriched in TFs with specific functional annotations.
all_mouse <- read.table("All Mouse names.txt")[,1]
depletion_mouse <- read.table("mouse.txt")[,1]all_mouse_names <- sapply(all_mouse, function(x) strsplit(as.character(x), "_")[[1]][1])
depletion_mouse_names <- sapply(depletion_mouse, function(x) strsplit(as.character(x), "_")[[1]][1])all_mouse_names_2 <- as.character(sapply(all_mouse_names, function(x) return(simpleCap(x))))
depletion_mouse_names_2 <- as.character(sapply(depletion_mouse_names, function(x) return(simpleCap(x))))write.table(all_mouse_names_2, file = "all_mouse_names.txt", quote = FALSE, row.names = FALSE, col.names = FALSE)
write.table(depletion_mouse_names_2, file = "depletion_mouse_names.txt", quote = FALSE, row.names = FALSE, col.names = FALSE)No significant functional pathway was observed and no GO was found enriched at \(0.01\) level of significance.
We check here whether depletion is enriched in TFs with specific functional annotations.
all_human <- read.table("All Human names.txt")[,1]
depletion_human <- read.table("Human.txt")[,1]all_human_names <- sapply(all_human, function(x) strsplit(as.character(x), "_")[[1]][1])
depletion_human_names <- sapply(depletion_human, function(x) strsplit(as.character(x), "_")[[1]][1])all_human_names_2 <- as.character(sapply(all_human_names, function(x) return(simpleCap(x))))
depletion_human_names_2 <- as.character(sapply(depletion_human_names, function(x) return(simpleCap(x))))write.table(all_human_names, file = "all_human_names.txt", quote = FALSE, row.names = FALSE, col.names = FALSE)
write.table(depletion_human_names, file = "depletion_human_names.txt", quote = FALSE, row.names = FALSE, col.names = FALSE)go <- read.delim2("go_human_depletion.tab")## Warning in read.table(file = file, header = header, sep = sep,
## quote = quote, : incomplete final line found by readTableHeader on
## 'go_human_depletion.tab'No pathway was enriched but the following GO annotation was moderatley enriched (although the q value was well above \(0.05\))
go## p.value q.value term_goid term_category term_level
## 1 0.00912109508275 0.109453140993 GO:0003713 m 4
## term_name
## 1 transcription coactivator activity
## members_input_overlap
## 1 3726; 4335; 6935; 7027; 7543; 9421; 9970; 64321
## members_input_overlap_geneids size effective_size
## 1 ZFX; JUNB; MNT; SOX17; NR1I3; HAND1; ZEB1; TFDP1 300 48