diff PSM_Z_Score.R @ 0:525f1318bb55 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_zscore commit 6ea2ae47fb74320afbb88a92e3fe40b5f8f86ad1

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PSM_Z_Score.R	Tue May 02 13:35:55 2017 -0400
@@ -0,0 +1,57 @@
+###############################################################################
+#                                                                             #
+# TestScript.R                                                                #
+#                                                                             #
+# I am using this to test the scripting language and passing parameters       #
+#                                                                             #
+# Created: 2017-04-12                                                         #
+#                                                                             #
+###############################################################################
+
+args <- commandArgs(TRUE) # Saves the parameters (command code)
+eval(parse(text=args))    # Runs the parameters
+# NOTE: This is extremely unsafe programming - any valid R code can run here
+
+#sprintf("z_cutoff is %s and ppm_tolerance is %s", z_cutoff, ppm_tolerance)
+#sprintf("Finally, the PSM report file is %s", psm_report)
+#sprintf("Oh, and the output file name is %s", output_psm_report)
+
+##### Support functions
+calc_z <- function(v=NULL, mu=NULL, sigma=NULL) {
+  return( (v-mu) / sigma )
+}
+
+##### Load Data
+data <- read.table(psm_report, 
+                   header = TRUE, 
+                   blank.lines.skip = TRUE, 
+                   fill = TRUE, 
+                   sep = "\t")
+#sprintf("data loaded")
+
+##### Local "confidence"
+values <- data$Precursor.m.z.Error..ppm.
+#sprintf("Number of values: %d", length(values))
+mu = mean(values)
+#sprintf("mean is %f", mu)
+sigma = sd(values)
+#sprintf("sigma is %f", sigma)
+precursor_z      <- calc_z(v=values, mu=mu, sigma=sigma)
+data$precursor_z <- precursor_z
+#sprintf("made the z list")
+write.table(data, file=output_psm_report, quote=FALSE, sep="\t", row.names=FALSE)
+#sprintf("file written")
+
+##### Global "confidence"
+ppm_min <- -ppm_tolerance
+ppm_max <- +ppm_tolerance
+zmin    <- calc_z(v=ppm_min, mu=mu, sigma=sigma)
+zmax    <- calc_z(v=ppm_max, mu=mu, sigma=sigma)
+area    <- (-z_cutoff - zmin) + (zmax - z_cutoff)
+nFalseHit <- sum(abs(precursor_z) > z_cutoff)
+n         <- length(values)
+propArea  <- area / (zmax - zmin)
+global_precursor_conf <- nFalseHit / (n * propArea)
+
+global_precursor_conf
+