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Tidy Meta Profiles using Bioconductor and the Tidyverse
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README.md

README.md

TeMPO

TeMPO is an R/Bioconductor package for producicing meta profiles (also known as meta genes, average profiles or average footprints) over one or more sets of genomic locations and signals. It takes as input various standard Bioconductor S4-classes and outputs simple data.frames for plotting with ggplot2 or manipulation using the tidyverse.

Installation

From Github

First install the dependencies from Bioconductor:

BiocManager::install(
    c("S4Vectors",
    "GenomicRanges",
    "rtracklayer"
    "BiocGenerics",
    "IRanges",
    "GenomeInfoDb",
    "BiocParallel",
    "BiocStyle",
    "AnnotationHub")
)

Then install TeMPO using devtools:

devtools::install_github("MalteThodberg/TeMPO")

From Bioconductor

Coming soon...!

Usage

library(TeMPO)
library(magrittr)
library(tidyr)
library(ggplot2)

data("CAGE_clusters")
data("CAGE_plus")
data("CAGE_minus")

# Stranded Meta-profile across enhancers:
P <- tidyMetaProfile(sites = subset(CAGE_clusters, 
                                    clusterType=="enhancer"),
                     forward = CAGE_plus,
                     reverse = CAGE_minus,
                     upstream=200,
                     downstream=200)

# Plot the resulting tibble with ggplot2:
P %>%
    gather(key="direction", value="score", sense, anti, factor_key=TRUE) %>%
    ggplot(aes(x=pos0, y=score, color=direction)) +
    geom_line(alpha=0.75) +
    scale_color_brewer("Direction", palette="Set1") +
    labs(x="Relative position from center", 
         y="Average Signal") +
    theme_minimal()

See the TeMPO vignette for full documentation!

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