setup_peaks_otucr <- function(peaks, datapath) {
if(dir.exists(datapath <- file.path(datapath, "otu"))) {
## Add Closed Reference OTUs, OTU Modules, and Bile Acids
if(file.exists(filename <- file.path(datapath, "peaks_OTU_CR.rds"))) {
peaks_new <- readRDS(filename)
peaks <- dplyr::bind_rows(peaks,
peaks_new[, names(peaks)])
}
peaks <- setup_peaks_otucr_module(peaks, datapath)
}
peaks
}
setup_peaks_otucr_module <- function(peaks, datapath) {
if(file.exists(filename <- file.path(datapath, "peaks_OTU_Module.rds"))) {
peaks_new <- dplyr::mutate(
readRDS(filename),
pheno = pheno_tissue("OTU", pheno), # prefix MEname by OTU.
longname = pheno,
output = pheno,
pheno_group = "OTU_Closed_Ref") # Change group from OTU_Module
# Drop grey module.
peaks_new <- dplyr::filter(
peaks_new,
pheno != "OTU.MEgrey")
peaks <- dplyr::bind_rows(peaks,
peaks_new[, names(peaks)])
}
peaks
}
setup_analyses_otucr <- function(analyses_tbl, peaks, datapath) {
if(dir.exists(datapath <- file.path(datapath, "otu"))) {
## Add Closed Reference OTUs, OTU Modules, and Bile Acids
if(file.exists(filename <- file.path(datapath, "analyses_OTU_CR.rds"))) {
analyses_new <-
dplyr::filter(
readRDS(filename),
output %in% peaks$output)
analyses_tbl <-
dplyr::bind_rows(analyses_tbl,
analyses_new[, names(analyses_tbl)])
}
analyses_tbl <- setup_analyses_otucr_module(analyses_tbl, peaks, datapath)
# Add model column to analyses_tbl
analyses_tbl <-
dplyr::mutate(
analyses_tbl,
model = ifelse(pheno_type == "OTU_Bin",
"binary",
"normal"))
analyses_tbl <-
dplyr::select(
analyses_tbl,
pheno:pheno_type, model, transf:ncol(analyses_tbl))
}
analyses_tbl
}
setup_analyses_otucr_module <- function(analyses_tbl, peaks, datapath) {
if(file.exists(filename <- file.path(datapath, "analyses_OTU_Module.rds"))) {
analyses_new <-
dplyr::filter(
dplyr::mutate(
readRDS(filename),
pheno = pheno_tissue("OTU", pheno),
longname = pheno,
output = pheno,
pheno_group = "OTU_Closed_Ref"),
output %in% peaks$output)
analyses_tbl <-
dplyr::bind_rows(analyses_tbl,
analyses_new[, names(analyses_tbl)])
}
analyses_tbl
}
setup_data_otucr <- function(pheno_data, peaks, datapath) {
if(dir.exists(datapath <- file.path(datapath, "otu"))) {
if(file.exists(filename <- file.path(datapath, "pheno_OTU_CR.rds"))) {
peaks_new <- dplyr::distinct(
dplyr::filter(
peaks,
pheno_group == "OTU_Closed_Ref",
pheno_type != "OTU_Module"),
pheno)
pheno_new <- readRDS(filename)
pheno_data <- setup_data_append(pheno_data, pheno_new, peaks_new)
}
pheno_data <- setup_data_otucr_module(pheno_data, peaks, datapath)
}
pheno_data
}
setup_data_otucr_module <- function(pheno_data, peaks, datapath) {
if(file.exists(filename <- file.path(datapath, "peaks_OTU_Module.rds"))) {
peaks_new <- dplyr::mutate(
dplyr::distinct(
dplyr::filter(
readRDS(filename),
pheno_type == "OTU_Module"),
pheno),
pheno_rename = pheno_tissue("OTU", pheno))
pheno_new <- readRDS(file.path(datapath, "pheno_OTU_Module.rds"))
pheno_data <- setup_data_append(pheno_data, pheno_new, peaks_new)
# Now put names we want for mrna
m <- match(peaks_new$pheno, colnames(pheno_data))
colnames(pheno_data)[m] <- peaks_new$pheno_rename
}
pheno_data
}
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