Analysis.DISEXP: Perform correlation analysis based on RNA distance and Gene...

In JackXu2333/rseAnalysis: Correlation analysis of RNA secondary structure mutation and differential expression

Description

Analysis.DISEXP is a complete analysis based on user selection of linear or log regression. The gene expression is calculated as the absolute differences between sampled and normal gene expression data. Analysis also export sets of graphs to facilitate in model selection and analysis result validation.

Usage

Analysis.DISEXP(
  dis.name,
  dis.distance,
  exp.tumor,
  exp.sample,
  method = "linear",
  showPlot = FALSE
)

Arguments

dis.name	Set of name of RNA distance
dis.distance	Set of RNA distance between mutate and original data
exp.tumor	Set of reads from gene expression from tumor samples
exp.sample	Set of reads from gene expression from normal samples (usually blood sample)
method	Selection of linear or gaussian log link function for regression (linear or log)
showPlot	TRUE and FALSE variable if TRUE the output image will be shown on the run

Value

Returns an S3 object of class DISEXP with results. list of output stats from the model

• stats

  • Correlation - Beta value of the regression model based on data

  • PValue - P value calculated associated with the correlation

  Show of four graph for validation

• plots

  • ScatterPlot plots of gene expression data on RNA distance data with fitted line

  • GeneExpressionBoxPlot Boxplot checking outliars on gene expression

  • RNADistanceBoxPlot Boxplot checking outliars on distance

  • RNADistanceDensityPlot Density plot on distance by different RNA

  • GeneExpressionDensityPlot Density plot on gene expression by different RNA

Author(s)

Sijie Xu, [e-mail]

Examples

disexp <- Analysis.DISEXP(
             dis.name = c("hsa-let-7a-1", "hsa-let-7a-1",
             "hsa-let-7a-3", "hsa-let-7a-3", "hsa-let-7a-3"),
             dis.distance = as.integer(c(10, 35, 91, 100, 92)),
             exp.tumor = c(98691, 49201, 57540, 148702, 97721),
             exp.sample = c(23495, 23310, 13274, 19337, 14389))

JackXu2333/rseAnalysis documentation built on Dec. 31, 2020, 1:10 p.m.