exploreData: Explore your Data

In kevincjnixon/BinfTools: Useful functions for standard analyses

Explore your Data

Description

This function generates a shiny App that allows you to interactively explore your data.

Usage

exploreData(res, counts, cond)

Arguments

res	A DESeq2 results object obtained from 'results(dds)' or a data.frame with the same column name values as a DESeq2 results object and rownames as genes. Can also be a named list of results objects.
counts	Normalized count matrix with rows as genes and columns as samples. Can also be a named list of count objects - ensure same order and names as the results object list.
cond	Character vector indicating conditions belonging to each sample (same order as colnames(counts)). Can also be a named list of condition vectors - ensure same order and names as results and counts object lists.

Value

A shiny app will be generated allowing you to explore your data interactively using BinfTools. Options to be selected: Dataset: the name of the dataset to look at (from your named list of objects). If no list is provided, defaults to 'data'. Control condition: The control condition for the current dataset (selected from cond) Absolute log2FoldChange Threshold: The log2 fold-change threshold for differentially expressed genes (defaults to log2(1.5)) P-value column: Use adjusted p-value (padj) or raw p-value (pvalue) P-value threshold: The significance threshold for differentially expressed genes (default=0.05) Gene to colour/label: Type in gene name to colour/label on volcano plot, MA plot, and heatmap (must match gene symbols in res/counts objects) Scale to point sizes: If yes, points in volcano plot and MA plot will be scaled to gene expression levels or significance, respectively species: Indicate the species of the data for pathway enrichment analyses Pathway Enrichment Sources: Select data source for pathway enrichment analysis Print top 10 terms: sig= top 10 significant terms from pathway enrichment. enr= top 10 enriched terms from pathway enrichment Pathway Keyword (GO only): Type in a key word for targeted analysis. Must have no spaces. Term names containing this string (even as part of a word) will be included for targeted analysis Count plot scaling: "none" = use valuse as is, "log10"= plot as log10(1+normcounts), "zscore"= plot z-score normcounts Count plot method: ind= use values from individual samples, mean= use average from samples in each condition, geoMean= use geometric mean from samples in each condition, median= use median from samples in each condition, perMean= percent mean of samples in each condition

kevincjnixon/BinfTools documentation built on July 10, 2024, 11:46 a.m.