hey there!
Can anyone help me with rMATS visualisation?
In R, following a page (https://bioconductor.org/packages/devel/bioc/vignettes/maser/inst/doc/Introduction.html) for rMATS visualisation, I am having trouble with the count values that I am getting by maser.
for my group, I ran
path <- system.file("C:/Program Files/R/R-4.3.1/library/maser/extdata", file.path("E:/alternate_dengue/rmats_analysis/rmats_o_sev_mild"), package = "maser")
sev_mild <- maser(path, c("severe", "mild"), ftype = "JC")
sev_mild
A Maser object with 0 splicing events.
Samples description:
Label=NA n= replicates
Label=NA n= replicates
Splicing events:
A3SS.......... 0 events
A5SS.......... 0 events
SE.......... 0 events
RI.......... 0 events
MXE.......... 0 events
The I shifted my files to the location of extdata and ran again
path <- system.file("extdata", file.path("MATS_output"), package = "maser")
sev_mild <- maser(path, c("severe", "mild"), ftype = "JC")
sev_mild
A Maser object with 190446 splicing events.
Samples description:
Label=severe n=21 replicates
Label=mild n=45 replicates
Splicing events:
A3SS.......... 11390 events
A5SS.......... 7909 events
SE.......... 131821 events
RI.......... 7637 events
MXE.......... 31689 events
Still, the values are not similar to what I got in as summary.txt file
JC
SE 139315
A5SS 8111
A3SS 11667
MXE 34588
RI 7677
expecting total JC values (first column)
Why aren't these values coming with code, how come they get changed?
Also, I went back to SE.MATS.JC.txt file, to see what is the actual count of SE events, but that is around 173000, and summary file says only about around 139000, and by maser package, I could only get 131000 around... How and Why?
