PLOTc2 | R Documentation |
plot 2 sets of RNA-seq and ribo-seq for comparison. It also contains a plot with transcript models.
PLOTc2(
YFG,
RNAbam1 = RNAseqBam1,
RNAbam2 = RNAseqBam2,
ribo1 = Ribo1,
ribo2 = Ribo2,
SAMPLE1 = S_NAME1,
SAMPLE2 = S_NAME2,
CDSonly = FALSE,
Extend = 50,
isoform,
uORF = NULL,
NAME = "",
uORFisoform
)
YFG |
Gene ID |
RNAbam1 |
Dataset 1 to plot. Default is RNAseqBam1 that was loaded by rna_bam.ribo. |
RNAbam2 |
Dataset 2 to plot. Default is RNAseqBam2 that was loaded by rna_bam.ribo. |
ribo1 |
riboseq dataset 1 |
ribo2 |
riboseq dataset 2 |
SAMPLE1 |
name of sample 1 |
SAMPLE2 |
name of sample 2 |
CDSonly |
TRUE or FALSE. Only plot CDS region or all riboseq reads in defined area. Default plot all riboseq reads in the defined area. |
Extend |
Integer. The number of extra nt ploted at the ends of the plots. |
isoform |
Integer. Which isoform to plot periodicity. |
uORF |
Gene ID for uORF |
NAME |
Name of the gene |
uORFisoform |
Isoform number of the uORF |
2 plots for RNAseq and Riboseq in 2 different genotypes/conditions.
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