Update peak_filtering_single_Sample.R

Data Processing/Psychencode_June2019/peak_filtering_single_Sample.R

@@ -1 +1,50 @@
-sfdasf
+```r
+setwd("C:\\Users\\z3526914\\OneDrive - UNSW\\Vafaee Lab\\Projects\\Deep Brain\\Training 2\\")
+# setwd("/Volumes/Data1/PROJECTS/DeepLearning/Test/")
+library(matrixStats)
+library(data.table)
+library(dplyr)
+
+# object name: 'peaks'
+filename <- "mergedPeakHeightMatrix_HumanFC"
+load(paste0(filename, ".rda"))
+val_th <- 0 # can be decided later
+
+# get meta-data to select columns (HumanFC: control samples)
+manifest <- fread("SYNAPSE_METADATA_MANIFEST.tsv", encoding = "UTF-8") %>% 
+ dplyr::select(c("individualID","specimenID")) %>% 
+ as.data.frame() 
+meta.data <- fread("R01MH105472_HumanFC_Metadata_Clinical_agecensored.csv", encoding = "UTF-8") %>% 
+ dplyr::select(c("individualID","daignosis")) %>% 
+ as.data.frame()
+control.specimens <- dplyr::inner_join(manifest, meta.data, by = "individualID") %>% 
+ dplyr::filter(daignosis == "Control") %>% 
+ dplyr::select("specimenID") %>% unlist(use.names = F)
+
+# only apply the selected patients
+new_peaks <- peaks %>% 
+ as.data.frame() %>% 
+ dplyr::select(control.specimens %>% 
+ as.vector()
+ ) %>% 
+ as.data.frame()
+
+new_peaks <- ifelse(new_peaks>val_th, 1, 0); rm(peaks)
+new_peaks <- ifelse(!is.na(new_peaks), new_peaks, 0) # replacing NAs with 0
+perc_th = ncol(new_peaks) * 0.5 # at least 50% of the samples should have at least non-zero signal
+peaks_1 <- which(rowSums2(new_peaks, na.rm = T) > perc_th)
+
+dat1 = data.frame(peak_coordinate = rownames(new_peaks)[peaks_1],
+ label = "1")
+dat0 = data.frame(peak_coordinate = rownames(new_peaks)[-peaks_1],
+ label = "0")
+
+dat = rbind(dat1, dat0)
+rownames(dat) = dat[,1]
+dat = dat[-1]
+
+binInfo <- as.data.frame(do.call(rbind,strsplit(rownames(dat), "_")))
+final.dat <- cbind(binInfo, rownames(dat), dat)
+colnames(final.dat) <- c("chr","start","end", "id", colnames(dat))
+fwrite(final.dat, paste0(filename, "_filtered_signle_label.BED"), row.names = F, quote = F, sep="\t")
+```