plotExonLength-methods {exomePeak2} | R Documentation |
This function plot the distribution of the exon length for peaks containing exons.
plotExonLength( sep, txdb = NULL, save_pdf_prefix = NULL, include_control_regions = TRUE, save_dir = "." ) ## S4 method for signature 'SummarizedExomePeak' plotExonLength( sep, txdb = NULL, save_pdf_prefix = NULL, include_control_regions = TRUE, save_dir = "." )
sep |
a |
txdb |
a |
save_pdf_prefix |
a |
include_control_regions |
a |
save_dir |
a |
If the SummarizedExomePeaks object contains LFC statistics, the significantly modified peaks with IP to input log2FC > 0 and GLM Wald test padj < .05 will be plotted .
If the SummarizedExomePeaks object contains interactive LFC statistics, both the hyper modification and hypo modification peaks with GLM Wald test p values < .05 will be plotted.
a ggplot object
### Make TxDb object from the gff file library(GenomicFeatures) GENE_ANNO_GTF = system.file("extdata", "example.gtf", package="exomePeak2") txdb <- makeTxDbFromGFF(GENE_ANNO_GTF) ### Load the example SummarizedExomPeak object f1 = system.file("extdata", "sep_ex_mod.rds", package="exomePeak2") sep <- readRDS(f1) ### Visualize the linear relationships between GC content and normalized reads count under different regions plotExonLength(sep,txdb)