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Edge r coeff #2885

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merged 5 commits into from
Feb 27, 2025
+21 −50
Merged

Edge r coeff #2885

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ce9b9ca
hardcode conditions diseased as coefficient
karishma-gangwani Feb 26, 2025
9c5f0ca
remove switch checkbox from UI
karishma-gangwani Feb 26, 2025
dbd1be3
Deleted flip_design_matrix from client and nodejs code
robinpaul85 Feb 26, 2025
86f3a12
Removed flip_design_matrix from edgeR code
robinpaul85 Feb 26, 2025
8702081
Put unused function in edgeR at the bottom
robinpaul85 Feb 26, 2025
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32 changes: 9 additions & 23 deletions client/plots/DEanalysis.js
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Original file line number Diff line number Diff line change
Expand Up @@ -160,25 +160,15 @@ class DEanalysis {
)
if (this.config.term) {
// Only when first confounding variable 1 has been selected, the option for a second confounding variable will be shown
inputs.push(
{
type: 'term',
configKey: 'term2',
chartType: 'DEanalysis',
usecase: { target: 'DEanalysis', detail: 'term' },
label: 'Confounding Factor 2',
title: 'Select confounding factors to adjust for in the analysis',
vocabApi: this.app.vocabApi
},
{
label: 'Switch model analysis order',
type: 'checkbox',
chartType: 'DEanalysis',
settingsKey: 'flip_design_matrix',
title: 'Causes design matrix to analyze confounding factors first before the groups',
boxLabel: ''
}
)
inputs.push({
type: 'term',
configKey: 'term2',
chartType: 'DEanalysis',
usecase: { target: 'DEanalysis', detail: 'term' },
label: 'Confounding Factor 2',
title: 'Select confounding factors to adjust for in the analysis',
vocabApi: this.app.vocabApi
})
}
}
}
Expand Down Expand Up @@ -710,7 +700,6 @@ export async function getPlotConfig(opts, app) {
pvaluetable: false,
adjusted_original_pvalue: 'adjusted',
method: 'edgeR',
flip_design_matrix: false,
VarGenes: 3000,
gene_ora: undefined,
gsea: undefined
Expand Down Expand Up @@ -807,9 +796,6 @@ async function runDEanalysis(self) {
input.tw = self.config.term
self.settings.method = 'edgeR' // When adjustment of confounding variables is selected, the method should always be a parmetric method such as edgeR
input.method = 'edgeR'
if (self.settings.flip_design_matrix) {
input.flip_design_matrix = self.settings.flip_design_matrix
}
}

if (self.config.term2) {
Expand Down
4 changes: 0 additions & 4 deletions server/routes/termdb.DE.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -234,10 +234,6 @@ values[] // using integer sample id
// If all elements in the confounding variable are equal, throw error as R script crashes if the confounding variable has only 1 level
throw 'Confounding variable 1 has only one value'
}
if (param.flip_design_matrix) {
// Flips design matrix in edgeR so as to analyze the confounding variable(s) first before the groups (when true)
expression_input.flip_design_matrix = param.flip_design_matrix
}
}

if (param.tw2) {
Expand Down
31 changes: 12 additions & 19 deletions server/utils/edge.R
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Original file line number Diff line number Diff line change
Expand Up @@ -30,13 +30,6 @@ filter_genes_by_global_variance <- function(read_counts, gene_id_symbols, num_va
return(list(read_counts = read_counts, gene_id_symbols = gene_id_symbols))
}

# Will implement this later
filter_genes_by_group_variance <- function(read_counts, gene_id_symbols, num_variable_genes, cases, controls) {
# Divide the read counts into two groups
case_read_counts <- read_counts[, cases]
control_read_counts <- read_counts[, controls]
}

# Read JSON input from stdin
read_json_time <- system.time({
con <- file("stdin", "r")
Expand Down Expand Up @@ -149,17 +142,13 @@ if (length(input$conf1) == 0) { # No adjustment of confounding factors
} else { # When input$conf1_mode == "discrete" keep the vector as string.
conf1 <- as.factor(input$conf1)
}

if (length(input$conf2) == 0) { # No adjustment of confounding factor 2
y$samples <- data.frame(conditions = conditions, conf1 = conf1)
model_gen_time <- system.time({
if (length(input$flip_design_matrix) == 0) { # When flip_design_matrix is not defined analyze groups (conditions) first
design <- model.matrix(~ conditions + conf1, data = y$samples)
} else { # When flip_design_matrix is defined analyze the confounding variable first
design <- model.matrix(~ conf1 + conditions, data = y$samples)
}
})
#cat("Time for making design matrix: ", model_gen_time[3], " seconds\n")
#cat("Time for making design matrix: ", model_gen_time[3], " seconds\n")
} else {
# Check the type of confounding variable 2
if (input$conf2_mode == "continuous") { # If this is float, the input conf2 vector should be converted into a numeric vector
Expand All @@ -169,14 +158,10 @@ if (length(input$conf1) == 0) { # No adjustment of confounding factors
}
y$samples <- data.frame(conditions = conditions, conf1 = conf1, conf2 = conf2)
model_gen_time <- system.time({
if (length(input$flip_design_matrix) == 0) { # When flip_design_matrix is not defined analyze groups (conditions) first
design <- model.matrix(~ conditions + conf1 + conf2, data = y$samples)
} else { # When flip_design_matrix is defined analyze the confounding variables first
design <- model.matrix(~ conf1 + conf2 + conditions, data = y$samples)
}
})
#cat("Time for making design matrix: ", model_gen_time[3], " seconds\n")
}
}

dispersion_time <- system.time({
y <- estimateDisp(y, design)
Expand All @@ -189,7 +174,7 @@ if (length(input$conf1) == 0) { # No adjustment of confounding factors
#cat("Fit time: ", fit_time[3], " seconds\n")

test_statistics_time <- system.time({
et <- glmLRT(fit, coef = 2)
et <- glmLRT(fit, coef = "conditionsDiseased")
})
#cat("Test statistics time: ", test_statistics_time[3], " seconds\n")
}
Expand All @@ -214,3 +199,11 @@ multiple_testing_correction_time <- system.time({

# Output results
toJSON(output)

#-----------------------------------#
# Will implement this later
filter_genes_by_group_variance <- function(read_counts, gene_id_symbols, num_variable_genes, cases, controls) {
# Divide the read counts into two groups
case_read_counts <- read_counts[, cases]
control_read_counts <- read_counts[, controls]
}
4 changes: 0 additions & 4 deletions shared/types/src/routes/termdb.DE.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -21,8 +21,6 @@ export type DERequest = {
tw2?: any
/** Number of variable genes (defined only for parametric DE methods) */
VarGenes?: number
/** Flips design matrix in edgeR so as to analyze the confounding variable(s) first before the groups */
flip_design_matrix: 'false' | 'true'
}

export type ExpressionInput = {
Expand Down Expand Up @@ -50,8 +48,6 @@ export type ExpressionInput = {
conf2_mode?: 'continuous' | 'discrete'
/** Number of variable genes to be included for DE analysis (optional) */
VarGenes?: number
/** Flips design matrix in edgeR so as to analyze the confounding variable(s) first before the groups */
flip_design_matrix: 'false' | 'true'
}

export type DEResponse = {
Expand Down