boxplot_element: Generate boxplots of every groups for a selected gene. Also...

In spell098/rnaseq_app:

Description

Generate boxplots of every groups for a selected gene. Also display stars for significance between groups

Usage

boxplot_element(selectedGene, names, expr.matrix, resultsSummary, results,
  color)

Arguments

selectedGene	Gene selected to display boxplots for each groups compared
names	A vector of the names of all samples
expr.matrix	A matrix of standardized data. Columns = samples, rows = genes,transcripts,CpG...
resultsSummary	A matrix of data from every gene that is significanlty different between at least two groups. Columns = samples, rows = genes,transcripts,CpG...
results	The results of every comparisons
color	The colors of all boxplot. One color for each group. Could be found in the function, not imported
names.unique	A vector of the names of all groups

Note

The function should require less input. names and names.unique could be removed by changing the code only the line from the selected gene should be imported, not every object to select it. This would remove expr.matrix,resultsSummary,results,selectedGene colors could also be found in the function. this would leave only a vector from expr.matrix(data) and a vector from resultsSummary(significance)

Author(s)

Simon J Pelletier

See Also

getGEO , Meta , Table , readGEOAnn

Examples

expr.matrix <- readRDS("data/expr_matrix_LGVD.rds")
results <- readRDS("data/expr_matrix_LGVD.rds")
selectedGene <- "ENSRNOG00000046319"
topTable3 <- readRDS("data/topTable3_LGVD.rds")
resultsSummary <- results_summary(results,topTable3)
color <- c("green","blue","red")
boxplot_element(selectedGene,expr.matrix,resultsSummary,results,color)

spell098/rnaseq_app documentation built on May 30, 2019, 7:57 a.m.