sediments: sediments: Prokaryotic Composition in Seafloor Sediments

In thoree/stat340: Data and functions for BIAS at NMBU

sediments: Prokaryotic Composition in Seafloor Sediments

Description

This data is from AQUAeD, a project at NMBU. Seafloor sediments from 12 selected sites along the Norwegian coast have been collected. Their prokaryotic composition were estimated by amplicon sequencing and subsequent bioinformatic analysis.

Usage

sediments

Format

A data frame with 12 observations (rows) and 4113 variables (columns).

	Column name	Data type	Description	Values
[,1]	Environment	character	Samples from 2 types of seafloor sediments	(Polluted, Natural)
[,2:4113]	Aaosphaeria...Zymoseptoria	numeric	Abundance of the various prokaryotic genera	(1 - 1475584)

The columns sediments[, 2:4113] are actual read-counts for various prokaryotic genera. A larger value means a larger abundance, but sequencing depth (total read-count) varies between the samples (rows). See sediments for the CLR-transformed data.

Source

The data is from the AQUAeD project (On-site monitoring of aquaculture impact on the environment by open-source nanopore eDNA analysis), a collaboration with NMBU, Institite of Marine Research (Havforskningsinstituttet), Akvaplan-niva, STIM, and Aquakompetanse AS.

References

Information of the AQUAeD project can be found here.

Examples

# A short summary of some of the variables
summary(sediments[, c(1, 100, 200, 300, 400, 500)])

# Boxplots for the abundance of Acephala and Aeromonas
par(mfrow = c(1, 2))
boxplot(Acephala ~ Environment, data = sediments_raw,
        col = c("sienna4", "tomato1"),
        main = "Acephala", ylab = "Abundance")
boxplot(Aeromonas ~ Environment, data = sediments_raw,
        col = c("sienna4", "tomato1"),
        main = "Aeromonas", ylab = "Abundance")

# Reset to default settings
par(mfrow = c(1, 1))

thoree/stat340 documentation built on June 30, 2024, 4:04 p.m.