plotCountMatrix: Plot count matrix of top gene/transcript Ids of selected...

In daewon-gong/NanoPlotR: Nanopore Sequencing Based RNA Modification Detection Visualization

Description

The modResults requires to be a dataframe with format of xPore's output format.

Usage

plotCountMatrix(modResults, modSites = c("A"), numTopIds = 20)

Arguments

modResults	RNA modification detection results in a dataframe.
modSites	Vector of modification sites that are included in the plot.
numTopIds	Number of top transcript/ids to display.

Details

The number of top n transcript/ids to display can be specified through the numTopIds parameter. The numTopIds paramter is Defaulted to 20

The desired modification sites can be given through the modSites parameter which requires a vector of characters specifying a RNA nucleotide. The function then plots a count matrix of top gene/transcript Ids of modifications sites where the middle kmer is part of vector modSites. Defaulted to c("A").

A ggplot of the count matrix is returned.

Value

a count matrix plot of inputted modSites and top gene/transcript id's ranked by DMR.

Author(s)

Dae-won Gong, [e-mail]

References

1. Hadley Wickham, Romain François, Lionel Henry and Kirill Müller (2021). dplyr: A Grammar of Data Manipulation. R package version 1.0.7. https://CRAN.R-project.org/package=dplyr

2. Pratanwanich, P. N., Yao, F., Chen, Y., Koh, C. W. Q., Wan, Y. K., Hendra, C., Poon, P., Goh, Y. T., Yap, P. M. L., Chooi, J. Y., Chng, W. J., Ng, S. B., Thiery, A., Goh, W. S. S., & Göke, J. (2021). Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore. Nature Biotechnology,39(11), 1394–1402. https://doi.org/10.1038/s41587-021-00949-w

3. H. Wickham. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York, 2016.

Examples

plotCountMatrix(RnaModificationResults, modSites = c("A"), numTopIds = 2)

daewon-gong/NanoPlotR documentation built on Dec. 19, 2021, 8:02 p.m.