In lpantano/bcbioSmallRna: small RNA-Seq Utilities

library(BiocStyle)
knitr::opts_chunk$set(tidy=FALSE,
                      dev="png",
                      message=FALSE, error=FALSE,
                      warning=TRUE)
library(knitr)
library(ggplot2)

# Set seed for reproducibility
set.seed(1454944673L)

theme_set(
    theme_light(base_size = 11L))
theme_update(
    legend.justification = "center",
    legend.position = "bottom")

library(isomiRs)
library(DEGreport)
library(bcbioSmallRna)

data(sbcb)
# bcbioSmallRnaDataSet
bcb <- sbcb

Get count matrix

You can get all the count matrix with the method mirna, isomir, cluster:

# for miRNAs
head(mirna(bcb))
# for clusters
head(cluster(bcb))
# for isomir
head(isomir(bcb))

By default this is the raw count data, however you can access a pre-computed normalized data using the second positional parameter log:

head(mirna(bcb, "log"))

Metrics

There are some important metris stored in the object that can be gotten with the following methods:

Adapter removal

These section shows how to get general stats for the adapter removal step.

To get the numbers of adapters removed at each position:

head(adapter(bcb)[["reads_by_pos"]])

As well, the total reads with adapter can be seen with:

adapter(bcb)[["reads_by_sample"]]

General metrics

All the metrics performed by bcbio can be seen with:

metrics(bcb)

Session

sessionInfo()

lpantano/bcbioSmallRna documentation built on March 5, 2020, 9:17 a.m.