From 86a3f370ff9b04a4822fdbd9e8b5d1642e9c2b1f Mon Sep 17 00:00:00 2001
From: moi-taiga <moi.t.nicholas@gmail.com>
Date: Thu, 13 Jun 2024 15:16:16 +0100
Subject: [PATCH] first pass

---
 R/pvalue.R | 56 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 56 insertions(+)
 create mode 100644 R/pvalue.R

diff --git a/R/pvalue.R b/R/pvalue.R
new file mode 100644
index 0000000..ecfd5fe
--- /dev/null
+++ b/R/pvalue.R
@@ -0,0 +1,56 @@
+#' @title pvalue
+#'
+#' @description
+#' Calculate the pvalue of the raw ppr score.
+#'
+#' @param sample_sce A Single Cell Experiment object,
+#' containing a matrix of your samples binary gene expression,
+#' which has been filtered to only include switching genes,
+#' using PathPinPointR::subset_switching_genes().
+#' @param sample_ppr An object of class ppr, must be the same sample.
+#' @param switching_genes Genes which switch through the trajectory,
+#'
+#' @return the pvalue of the raw ppr score.
+#'
+#' @export
+#'
+
+calculate_pvalue <- function(sample_sce, sample_ppr, switching_genes) {
+  # Find the maximum raw ppr score.
+  max_raw_ppr_score <- max(sample_ppr$sample_flat)
+
+  ## produce 2000 random samples, and extract their max ppr scores.
+
+  # Extract the binary matrix
+  bin_mat <- sample_sce@assays@data$binary
+
+  # Create a vector to store the max ppr scores
+  random_max_raw_ppr_scores <- numeric(100)
+
+  for (i in 1:100) {
+    # Shuffle the row names in place
+    rownames(bin_mat) <- sample(rownames(bin_mat))
+
+    # Update the binary matrix within the sample object
+    sample_sce@assays@data$binary <- bin_mat
+
+    # Perform prediction
+    random_sample_ppr <- ppr_predict_position(sample_sce, switching_genes)
+
+    # Extract the maximum raw ppr score
+    random_max_raw_ppr_scores[i] <- max(random_sample_ppr$sample_flat)
+  }
+
+  # calculate the distance of the max_raw_ppr_score from the mean of random_max_raw_ppr_scores
+  # using standard deviations of the random samples
+
+  # calculate the standand deviation of the random max ppr scores
+    sd_random_max_raw_ppr_scores <- sd(random_max_raw_ppr_scores)
+
+    # calculate the z-score
+    z_score <- (max_raw_ppr_score - mean(random_max_raw_ppr_scores)) / sd_random_max_raw_ppr_scores
+
+#pnorm?
+    return(pnorm(z_score))
+
+}
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