From b6dd36b5738de4575b2da09905b3c899f02b6027 Mon Sep 17 00:00:00 2001 From: Julie Livingstone Date: Tue, 6 Feb 2024 08:20:09 -0800 Subject: [PATCH] indentation changes --- OutlierDetectionAlgorithm/5.Simulated_Data_5method.R | 9 ++++----- .../8.Significant_Outlier_Pvalue_Calculation.R | 4 ++-- 2 files changed, 6 insertions(+), 7 deletions(-) diff --git a/OutlierDetectionAlgorithm/5.Simulated_Data_5method.R b/OutlierDetectionAlgorithm/5.Simulated_Data_5method.R index e4c4aec..2f4260e 100644 --- a/OutlierDetectionAlgorithm/5.Simulated_Data_5method.R +++ b/OutlierDetectionAlgorithm/5.Simulated_Data_5method.R @@ -70,7 +70,7 @@ if (patients.to.remove > 0) { sample.number <- patient.part negative.simulated.sum <- negative.simulated.sum[, patient.part] fpkm.tumor.symbol.filter <- fpkm.tumor.symbol.filter[,patient.part] - } + } # Define a minimum value set.seed(42) @@ -281,7 +281,6 @@ data.cosine.negative.t <- t(data.cosine.negative); data.cosine.negative.t <- data.frame(data.cosine.negative.t); colnames(data.cosine.negative.t) <- c('cosine', 'distribution'); - # 1, 2, 3, 4 quantify.outliers <- function(x, methods = 'mean', trim = 0, exclude.zero = FALSE) { x.na <- na.omit(as.numeric(x)); @@ -428,9 +427,9 @@ kmean.simulated.negative.1M <- data.frame(t(data.fraction.kmean)); ### Final gene-wise matrix ##### gene.zrange.fraction.negative.simulated.sum.1M <- cbind( mean.simulated.negative.1M$zrange, - median.simulated.negative.1M$zrange, - trimmean.simulated.negative.1M$zrange, - kmean.simulated.negative.1M$fraction + median.simulated.negative.1M$zrange, + trimmean.simulated.negative.1M$zrange, + kmean.simulated.negative.1M$fraction ) rownames(gene.zrange.fraction.negative.simulated.sum.1M) <- rownames(negative.simulated.sum); colnames(gene.zrange.fraction.negative.simulated.sum.1M) <- c('zrange.mean', 'zrange.median', 'zrange.trimmean', 'fraction.kmean'); diff --git a/OutlierDetectionAlgorithm/8.Significant_Outlier_Pvalue_Calculation.R b/OutlierDetectionAlgorithm/8.Significant_Outlier_Pvalue_Calculation.R index bd46688..f655baf 100644 --- a/OutlierDetectionAlgorithm/8.Significant_Outlier_Pvalue_Calculation.R +++ b/OutlierDetectionAlgorithm/8.Significant_Outlier_Pvalue_Calculation.R @@ -35,11 +35,11 @@ p.value.all <- NULL for (i in 1:length(files)) { load( file = files[i] - ) + ) assign( x = 'variable.name', value = paste('gene.rank.p.value.one.gene', patients.to.remove, sep = '.') - ) + ) p.value.all <- rbind( p.value.all, get(x = variable.name)