SequencingHeatmap: Sequencing Data Heatmap Creation

In TomNash/sequencingHeatmap: Heatmap Creation for RNA Sequencing Data

Description

This function allows you to create heatmaps from a sequencing output spreadsheet.

Usage

SequencingHeatmap(input.file, sheet, data.columns, subsets.directory, id.method,
  cutoff.p = 0.4, base.mean.count = 15, top)

Arguments

input.file	The path to the sequencing output spreadsheet (.xlsx), i.e. sequencing="path/to/output.xlsx"
sheet	The sheet number in the spreadsheet with data, i.e sheet=1
data.columns	The column range of data to use, i.e. data.columns=5:31
subsets.directory	The path to the directory which contains files of genes of interest, i.e. subsets.directory="path/to/inputs/"
id.method	The method of identifying each gene. It must be either id.method="symbol" or id.method="geneid"
base.mean.count	Threshold for omitting genes, all genes with expression below this value will not be included, default is set to 15 but set to 0 to include all genes
top	(optional) The number of top genes to select, filtered by adjusted p-value. Can use multiple values for one run, i.e. top=100 or top=c(100,125,150)

Details

Formatting of an input file:
Method of clustering the results, either "gene", "sample", or "both"
Title of the heatmap plot
GENE1
GENE2
GENE3
...

Example input file:
gene
Sample Graph Title
SFRP2
CD4
BRCA1
...

Outputs (found in ./sequencingHeatmap-output):
PDF, TIFF, FIG, and EPS of heatmaps
CSV of fold-changes
* All file names correspond to those in the provided inputs directory

Directory structure for inputs and resultings outputs with given args:

.
|---sequencingoutput.xlsx                 # input.file='sequencingoutput.xlsx'
|---experiment1                      # subsets.directory='experiment1'
|   |---genelist1.txt
|----sequencingHeatmap-output
|   |---experiment1
|       |---genelist1-top100.pdf     # top=c(100,125)
|       |---genelist1-top125.pdf     
|       |---genelist1-top100.tiff
|       |---genelist1-top125.tiff
|       |---genelist1-top100.eps
|       |---genelist1-top125.eps
|       |---genelist1-top100.fig
|       |---genelist1-top125.fig
|       |---genelist1-top100-foldChange.csv
|       |---genelist1-top125-foldChange.csv
|       |---sequencingoutput-genelist1-top100-truncated.csv
|       |---sequencingoutput-genelist1-top125-truncated.csv

Examples

## Not run: 

library(sequencingHeatmap)
sequencingHeatmap(sequencing="sequencingoutput.xlsx", sheet=1, data.columns=5:14,
subsets.directory="experiment1", id.method="symbol", top=c(100,125,150))

## End(Not run)

TomNash/sequencingHeatmap documentation built on May 9, 2019, 5:10 p.m.