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comparison R_functions/outlier_trimming.R @ 0:cb54350e76ae draft default tip

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author jason-ellul
date Wed, 01 Jun 2016 03:24:56 -0400
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1 # Finding outliers by standard deviation
2
3 # Get samples whose pc1 OR pc2 values lie more than 'numsds' s.devs
4 # away from the sample median for that pc.
5 outliers_by_sd = function(pca_data, xsamples, numsds) {
6 pc1_outliers = find_outliers(pca_data$values[, 1], numsds)
7 pc2_outliers = find_outliers(pca_data$values[, 2], numsds)
8 all_outliers = union(pc1_outliers, pc2_outliers)
9 return(all_outliers)
10 }
11
12 # compute outliers
13 # Returns indices of all samples which lie more than
14 # 'numsds' s.devs away from the sample median
15 find_outliers = function(input_data, numsds) {
16 lower = median(input_data) - numsds*sd(input_data)
17 upper = median(input_data) + numsds*sd(input_data)
18
19 outliers = which(input_data < lower | input_data > upper)
20 return(outliers)
21 }