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index.Rmd
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index.Rmd
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---
title: "Home"
site: workflowr::wflow_site
output:
workflowr::wflow_html:
toc: false
editor_options:
chunk_output_type: console
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(
autodep = TRUE,
echo = TRUE,
warning = FALSE,
message = FALSE
)
```
```{r}
library(tidyverse)
library(tidygraph)
library(ggraph)
```
```{r}
samples <- read_csv("data/samples.csv") %>%
distinct(sampleName, .keep_all = TRUE) %>%
dplyr::select(sample = sampleName, sampleID, genotype) %>%
mutate(genotype = factor(genotype, levels = c("WT", "Het", "Hom")))
```
This dataset is an analysis of RNASeq data from a 3-way comparison of WT zebrafish with Heterozygous mutants (*psen2^S4Ter/+^*) and Homozygous mutants *psen2^S4Ter/S4Ter^*.
The *psen2^S4Ter^* mutant allele is expected to be a premature termination of the *psen2* gene, but instead an alternate downstream start site resulted in a near full-length transcript with significant similarity to a conventional Early Onset Familial Alzhemier's Disease mutation.
The expected comparisons were intended to be a three-way group comparison, however the final model was defined by fitting the wild-type samples, differences between heterozygotes and wild-type, followed by the difference between the two mutant genotypes
```{r plotLayout, fig.width=4, fig.height=4}
create_ring(3) %>%
mutate(
name = paste0(levels(samples$genotype), "\n(n = 4)"),
name = factor(name, levels = name)
) %>%
activate(edges) %>%
mutate(comparison = c("Het Vs WT", "Hom Vs Het", "Hom Vs WT")) %>%
dplyr::filter(comparison != "Hom Vs WT") %>%
ggraph(layout = "kk") +
geom_edge_link2(
aes(label = comparison),
angle_calc = "along",
label_dodge = unit(0.02, "npc"),
start_cap = circle(0.09, "npc"),
end_cap = circle(0.09, "npc"),
label_size = 5,
arrow = arrow(
length = unit(0.06, "npc"),
ends = "both",
type = "closed"
)
) +
geom_node_label(
aes(label = name, colour = name),
size = 5,
fill = rgb(1,1,1,0.7),
label.padding = unit(0.4, "lines")
) +
scale_y_continuous(expand = expand_scale(0.1)) +
scale_x_continuous(expand = expand_scale(0.1)) +
theme_void() +
theme(
legend.position = "none"
)
```
All samples were female, 6 months old and raised in the same tank as a family, to minimise variability.
This age represents sexual maturity and is expected to model a pre-symptomatic brain.
Fish were all killed and genotyped by tail-clipping on 07-07-2016.
RNAseq was performed on total RNA (i.e. ribo-reduced) from whole brain tissue, with $n=4$ samples in each group.
Sequencing was performed by the sequencing facility at the Centre for Cancer Biology in Adelaide, using an Illimuna NextSeq.
Reads were provided in as paired-end, 150bp reads.
1. [Bash Pipeline](0_bashPipeline.html)
2. [Quality Assesment](1_QC.html)
3. [Differential Expression Analysis](2_DifferentialExpression.html)
4. Enrichment Analysis
a. [Mutant Vs Wild Type](3_Enrichment_MutantVsWT.html)
b. [Homozygous Vs Heterzygous Mutants](3_Enrichment_HomVsHet.html)