From 29617eef8c2643e9d600a00619bfbdea1486a2ed Mon Sep 17 00:00:00 2001 From: Lazzat Aibekova <45805067+lazzataibekova@users.noreply.github.com> Date: Fri, 7 Jun 2019 10:43:51 +0900 Subject: [PATCH] Add files via upload --- DE_varroa.Rmd | 8 +- DE_varroa_microbiome.csv | 26 +- DE_varroa_mite.Rmd | 10 +- Plots.Rmd | 29 +- Plots.nb.html | 128 +- gene_level_DE_analysis.Rmd | 482 + genebank_gene_map.csv | 30209 +++++++++++++++++++++++++++++++++++ 7 files changed, 30845 insertions(+), 47 deletions(-) create mode 100644 gene_level_DE_analysis.Rmd create mode 100644 genebank_gene_map.csv diff --git a/DE_varroa.Rmd b/DE_varroa.Rmd index 2c99ce1..8d28bee 100644 --- a/DE_varroa.Rmd +++ b/DE_varroa.Rmd @@ -157,7 +157,7 @@ up_down_regulated ### Аrresting vs. pre-laying ```{r} -so <- sleuth_prep(dplyr::filter(samples, shortName %in% c("phoretic", "prelaying")), extra_bootstrap_summary = TRUE) +so <- sleuth_prep(dplyr::filter(samples, shortName %in% c("arresting", "prelaying")), extra_bootstrap_summary = TRUE) so <- sleuth_fit(so, ~condition, 'full') so <- sleuth_fit(so, ~1, 'reduced') so <- sleuth_lrt(so, 'reduced', 'full') @@ -189,7 +189,7 @@ up_down_regulated ### Pre-laying vs. Laying ```{r} -so <- sleuth_prep(dplyr::filter(samples, shortName %in% c("phoretic", "laying")), extra_bootstrap_summary = TRUE) +so <- sleuth_prep(dplyr::filter(samples, shortName %in% c("prelaying", "laying")), extra_bootstrap_summary = TRUE) so <- sleuth_fit(so, ~condition, 'full') so <- sleuth_fit(so, ~1, 'reduced') so <- sleuth_lrt(so, 'reduced', 'full') @@ -204,8 +204,8 @@ models(so) ``` Number of Differentially expressed genes (TRUE): ```{r} -so = sleuth_wt(so, 'conditionphoretic') -results_table = sleuth_results(so, 'conditionphoretic') +so = sleuth_wt(so, 'conditionprelaying') +results_table = sleuth_results(so, 'conditionprelaying') Number_DE_genes = table(results_table$qval <= 0.05) Number_DE_genes ``` diff --git a/DE_varroa_microbiome.csv b/DE_varroa_microbiome.csv index 83e31e2..ebaed77 100644 --- a/DE_varroa_microbiome.csv +++ b/DE_varroa_microbiome.csv @@ -1,13 +1,13 @@ -Stages,M_DE,M_up-regulated,M_down-regulated,V_DE,V_up-regulated,V_down-regulated,V2_DE,V2_up-regulated,V2_down-regulated -males vs young,5397,1596,3801,19220,8328,10892,8069,2641,5428 -Young vs Phoretic,2852,1570,1282,12769,6846,5923,3374,1763,1611 -Phoretics vs caged,1,0,1,0,0,0,23,13,10 -Phoretic vs arresting,68,19,49,3514,1288,2226,100,36,64 -Arrest vs pre-laying,2866,1527,1339,9458,4769,4689,3715,1890,1825 -Pre-laying vs. Laying,4247,1951,2296,2683,1795,888,5666,2654,3012 -Laying vs. post-laying,2803,978,1105,9456,4077,5379,2851,1264,1587 -Post-laying vs. Emerging,619,322,297,3536,2135,1401,619,322,297 -Post-laying vs. Non-laying,5,3,2,2,2,0,4,1,3 -Laying vs Non-laying,2203,1903,1110,13065,5738,7327,2203,1093,1110 -Emerging vs Phoretic,571,219,352,1492,889,603,571,219,352 -Emerging vs Young,1870,1011,859,8947,4465,4482,1870,1011,859 \ No newline at end of file +Stages,M_DE,M_up-regulated,M_down-regulated,V_DE,V_up-regulated,V_down-regulated,V2_DE,V2_up-regulated,V2_down-regulated,V_gene_DE,V_gene_up-regulated,V_gene_down-regulated +males vs young,5397,1596,3801,19220,8328,10892,8069,2641,5428,5759,2692,3067 +Young vs Phoretic,2852,1570,1282,12769,6846,5923,3374,1763,1611,4796,2463,2333 +Phoretics vs caged,1,0,1,0,0,0,23,13,10,51,27,24 +Phoretic vs arresting,68,19,49,3514,1288,2226,100,36,64,35,11,24 +Arrest vs pre-laying,1039,447,592,9458,4769,4689,2020,962,1058,3215,1647,1568 +Pre-laying vs. Laying,432,288,144,2683,1795,888,760,502,258,1473,799,674 +Laying vs. post-laying,2083,978,1105,9456,4077,5379,2851,1264,1587,3757,1741,2016 +Post-laying vs. Emerging,619,322,297,3536,2135,1401,700,292,408,1405,752,653 +Post-laying vs. Non-laying,5,3,2,2,2,0,4,1,3,2,2,0 +Laying vs Non-laying,2203,1093,1110,13065,5738,7327,3433,1529,1904,4602,2038,2564 +Emerging vs Phoretic,571,219,352,1492,889,603,600,352,248,866,448,418 +Emerging vs Young,1870,1011,859,8947,4465,4482,2505,1383,1122,4070,2135,1935 \ No newline at end of file diff --git a/DE_varroa_mite.Rmd b/DE_varroa_mite.Rmd index 513602c..f5b011c 100644 --- a/DE_varroa_mite.Rmd +++ b/DE_varroa_mite.Rmd @@ -1,5 +1,5 @@ --- -title: "Varroa" +title: "Varroa re-mapped" author: "Lazzat Aibekova" date: "6/04/2019" output: html_document @@ -156,7 +156,7 @@ up_down_regulated ### Аrresting vs. pre-laying ```{r} -so <- sleuth_prep(dplyr::filter(samples, shortName %in% c("phoretic", "prelaying")), extra_bootstrap_summary = TRUE) +so <- sleuth_prep(dplyr::filter(samples, shortName %in% c("arresting", "prelaying")), extra_bootstrap_summary = TRUE) so <- sleuth_fit(so, ~condition, 'full') so <- sleuth_fit(so, ~1, 'reduced') so <- sleuth_lrt(so, 'reduced', 'full') @@ -188,7 +188,7 @@ up_down_regulated ### Pre-laying vs. Laying ```{r} -so <- sleuth_prep(dplyr::filter(samples, shortName %in% c("phoretic", "laying")), extra_bootstrap_summary = TRUE) +so <- sleuth_prep(dplyr::filter(samples, shortName %in% c("prelaying", "laying")), extra_bootstrap_summary = TRUE) so <- sleuth_fit(so, ~condition, 'full') so <- sleuth_fit(so, ~1, 'reduced') so <- sleuth_lrt(so, 'reduced', 'full') @@ -203,8 +203,8 @@ models(so) ``` Number of Differentially expressed genes (TRUE): ```{r} -so = sleuth_wt(so, 'conditionphoretic') -results_table = sleuth_results(so, 'conditionphoretic') +so = sleuth_wt(so, 'conditionprelaying') +results_table = sleuth_results(so, 'conditionprelaying') Number_DE_genes = table(results_table$qval <= 0.05) Number_DE_genes ``` diff --git a/Plots.Rmd b/Plots.Rmd index 8f292bc..ca02d50 100644 --- a/Plots.Rmd +++ b/Plots.Rmd @@ -7,33 +7,54 @@ data = read.csv("/Users/lazzataibekova/Dropbox (OIST)/varroa microbiome/DE_varro data ``` - +###Varroa vs Microbiome ```{r} plot(data$V_DE, data$M_DE, xlab = "Varroa genes", ylab = "Microbiome genes", main = "Total number of DEG") cor(data$V_DE, data$M_DE) ``` - +#Up-regulated genes ```{r} plot(data$V_up.regulated, data$M_up.regulated, xlab = "Varroa genes", ylab = "Microbiome genes", main = "Number of up-regulated genes") cor(data$V_up.regulated, data$M_up.regulated) ``` - +#Down-regulated ```{r} plot(data$V_down.regulated, data$M_down.regulated, xlab = "Varroa genes", ylab = "Microbiome genes", main = "Number of down-regulated genes") cor(data$V_down.regulated, data$M_down.regulated) ``` +###Re-mapped Varroa vs Microbiome ```{r} plot(data$V2_DE, data$M_DE, xlab = "Varroa genes", ylab = "Microbiome genes", main = "Total number of DEG (re-mapped)") cor(data$V2_DE, data$M_DE) ``` +#Up-regulated genes ```{r} plot(data$V2_up.regulated, data$M_up.regulated, xlab = "Varroa genes", ylab = "Microbiome genes", main = "Number of up-regulated genes (re-mapped)") cor(data$V2_up.regulated, data$M_up.regulated) ``` - +#Down-regulated genes ```{r} plot(data$V2_down.regulated, data$M_down.regulated, xlab = "Varroa genes", ylab = "Microbiome genes", main = "Number of down-regulated genes (re-mapped)") cor(data$V2_down.regulated, data$M_down.regulated) ``` +###Gene-level analysis +```{r} +plot(data$V2_DE, data$V_gene_DE, xlab = "Re-mapped DE Varroa genes", ylab = "Gene-level DE VArroa", main = "Varroa DE vs Gene-level DE") +cor(data$V2_DE, data$V_gene_DE) +``` +#Microbiome vs Varroa (gene-level) +```{r} +plot(data$V_gene_DE, data$M_DE, xlab = "Gene-level DE Varroa", ylab ="Microbiome DE", main = "Varroa Gene-level DE vs Microbiome DE") +cor(data$V_gene_DE, data$M_DE) +``` +```{r} +plot(data$V_gene_up.regulated, data$M_up.regulated, xlab = "Gene-level up-regulated VArroa", ylab = "Microbiome up-regulated", main = "Varroa Gene-level vs Microbiome") +cor(data$V_gene_up.regulated, data$M_up.regulated) +``` + +```{r} +plot(data$V_gene_down.regulated, data$M_down.regulated, xlab = "Gene-level down-regulated VArroa", ylab = "Microbiome down-regulated", main = "Varroa Gene-level vs Microbiome") +cor(data$V_gene_down.regulated, data$M_down.regulated) +``` \ No newline at end of file diff --git a/Plots.nb.html b/Plots.nb.html index 6fbf60a..c5c1fe7 100644 --- a/Plots.nb.html +++ b/Plots.nb.html @@ -250,112 +250,198 @@

R Notebook

data = read.csv("/Users/lazzataibekova/Dropbox (OIST)/varroa microbiome/DE_varroa_microbiome.csv")
 data
- +
+
+

Varroa vs Microbiome

plot(data$V_DE, data$M_DE, xlab = "Varroa genes", ylab = "Microbiome genes", main = "Total number of DEG")
-

+

cor(data$V_DE, data$M_DE)
- -
[1] 0.7540207
+ +
[1] 0.9415581
+
+
+

Up-regulated genes

plot(data$V_up.regulated, data$M_up.regulated, xlab = "Varroa genes", ylab = "Microbiome genes", main = "Number of up-regulated genes")
-

+

cor(data$V_up.regulated, data$M_up.regulated)
- -
[1] 0.7598868
+ +
[1] 0.9475617
+
+
+

Down-regulated

plot(data$V_down.regulated, data$M_down.regulated, xlab = "Varroa genes", ylab = "Microbiome genes", main = "Number of down-regulated genes")
-

+

cor(data$V_down.regulated, data$M_down.regulated)
- -
[1] 0.7331989
+ +
[1] 0.9045221
+
+

Re-mapped Varroa vs Microbiome

plot(data$V2_DE, data$M_DE,  xlab = "Varroa genes", ylab = "Microbiome genes", main = "Total number of DEG (re-mapped)")
-

+

cor(data$V2_DE, data$M_DE)
- -
[1] 0.9840727
+ +
[1] 0.9903246
+ +
+
+
+

Up-regulated genes

+ 
plot(data$V2_up.regulated, data$M_up.regulated,  xlab = "Varroa genes", ylab = "Microbiome genes", main = "Number of up-regulated genes (re-mapped)")
-

+

cor(data$V2_up.regulated, data$M_up.regulated)
- -
[1] 0.898323
+ +
[1] 0.9664128
+
+
+

Down-regulated genes

plot(data$V2_down.regulated, data$M_down.regulated,  xlab = "Varroa genes", ylab = "Microbiome genes", main = "Number of down-regulated genes (re-mapped)")
-

+

cor(data$V2_down.regulated, data$M_down.regulated)
- -
[1] 0.9947204
+ +
[1] 0.9945545
+ + + +
+

Gene-level analysis

+ + + +
plot(data$V2_DE, data$V_gene_DE, xlab = "Re-mapped DE Varroa genes", ylab = "Gene-level DE VArroa", main = "Varroa DE vs Gene-level DE")
+ + +

+ + +
cor(data$V2_DE, data$V_gene_DE)
+ + +
[1] 0.8925148
+ + + +
+
+
+

Microbiome vs Varroa (gene-level)

+ + + +
plot(data$V_gene_DE, data$M_DE, xlab = "Gene-level DE Varroa", ylab ="Microbiome DE", main = "Varroa Gene-level DE vs Microbiome DE")
+ + +

+ + +
cor(data$V_gene_DE, data$M_DE)
+ + +
[1] 0.9021928
+ + + + +
plot(data$V_gene_up.regulated, data$M_up.regulated, xlab = "Gene-level up-regulated VArroa", ylab = "Microbiome up-regulated", main = "Varroa Gene-level vs Microbiome")
+ + +

+ + +
cor(data$V_gene_up.regulated, data$M_up.regulated)
+ + +
[1] 0.9605862
+ + +
plot(data$V_gene_down.regulated, data$M_down.regulated, xlab = "Gene-level down-regulated VArroa", ylab = "Microbiome down-regulated", main = "Varroa Gene-level vs Microbiome")
+ + +

+ + +
cor(data$V_gene_down.regulated, data$M_down.regulated)
+ + +
[1] 0.8274113
+ + +
-
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+
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diff --git a/gene_level_DE_analysis.Rmd b/gene_level_DE_analysis.Rmd new file mode 100644 index 0000000..9bfdbb5 --- /dev/null +++ b/gene_level_DE_analysis.Rmd @@ -0,0 +1,482 @@ +--- +title: "Gene-level DE analysis" +output: html_document +--- + +```{r setup, include=FALSE} +knitr::opts_chunk$set(echo = TRUE) +``` + +```{r} +library(sleuth) +library(tidyverse) + +``` + +```{r sleuth} +samples <- tibble(id = dir(file.path("mondet/kallisto_mite"))) %>% mutate(path = paste0("mondet/kallisto_mite/", id)) %>% + left_join(read_tsv("mondet/treatments.tsv", col_types = cols())) %>% mutate(sample = id, condition = shortName) +``` + +#transcript to gene table +```{r} +t2g = read.csv("/Users/lazzataibekova/Dropbox (OIST)/varroa microbiome/genebank_gene_map.csv", header=T) +``` + +### Comparing males vs young +```{r} +so <- sleuth_prep(dplyr::filter(samples, shortName %in% c("young", "males")), target_mapping = t2g,aggregation_column = 'ens_gene', gene_mode = T) +``` + +```{r} +plot_pca(so, color_by = 'condition') +``` + +```{r} +so <- sleuth_fit(so, ~condition, 'full') +so <- sleuth_fit(so, ~1, 'reduced') +so <- sleuth_lrt(so, 'reduced', 'full') +``` + +```{r} +sleuth_table <- sleuth_results(so, 'reduced:full', 'lrt') +sleuth_significant <- dplyr::filter(sleuth_table, qval <= 0.05) +dim(sleuth_significant) +head(sleuth_significant) +``` + +```{r} +models(so) +``` +Number of Differentially expressed genes (TRUE): +```{r} +so = sleuth_wt(so, 'conditionyoung') +results_table = sleuth_results(so, 'conditionyoung') +Number_DE_genes = table(results_table$qval <= 0.05) +Number_DE_genes +``` +```{r} +DE_genes = subset(results_table, qval <= 0.05) +DE_genes +up_down_regulated = table(DE_genes$b > 0) +up_down_regulated +``` +###Young vs Phoretic + +```{r} +so <- sleuth_prep(dplyr::filter(samples, shortName %in% c("young", "phoretic")), target_mapping = t2g,aggregation_column = 'ens_gene', gene_mode = T) +``` + +```{r} +plot_pca(so, color_by = 'condition') +``` + +```{r} +so <- sleuth_fit(so, ~condition, 'full') +so <- sleuth_fit(so, ~1, 'reduced') +so <- sleuth_lrt(so, 'reduced', 'full') +``` + +```{r} +sleuth_table <- sleuth_results(so, 'reduced:full', 'lrt') +sleuth_significant <- dplyr::filter(sleuth_table, qval <= 0.05) +dim(sleuth_significant) +head(sleuth_significant) +``` + +```{r} +models(so) +``` +Number of Differentially expressed genes (TRUE): +```{r} +so = sleuth_wt(so, 'conditionyoung') +results_table = sleuth_results(so, 'conditionyoung') +Number_DE_genes = table(results_table$qval <= 0.05) +Number_DE_genes +``` +```{r} +DE_genes = subset(results_table, qval <= 0.05) +DE_genes +up_down_regulated = table(DE_genes$b > 0) +up_down_regulated +``` +### Phoretics vs caged +```{r} +so <- sleuth_prep(dplyr::filter(samples, shortName %in% c("phoretic", "phoreticCaged")), target_mapping = t2g,aggregation_column = 'ens_gene', gene_mode = T) +``` + +```{r} +plot_pca(so, color_by = 'condition') +``` + +```{r} +so <- sleuth_fit(so, ~condition, 'full') +so <- sleuth_fit(so, ~1, 'reduced') +so <- sleuth_lrt(so, 'reduced', 'full') +``` + +```{r} +sleuth_table <- sleuth_results(so, 'reduced:full', 'lrt') +sleuth_significant <- dplyr::filter(sleuth_table, qval <= 0.05) +dim(sleuth_significant) +head(sleuth_significant) +``` + +```{r} +models(so) +``` +Number of Differentially expressed genes (TRUE): +```{r} +so = sleuth_wt(so, 'conditionphoreticCaged') +results_table = sleuth_results(so, 'conditionphoreticCaged') +Number_DE_genes = table(results_table$qval <= 0.05) +Number_DE_genes +``` +```{r} +DE_genes = subset(results_table, qval <= 0.05) +DE_genes +up_down_regulated = table(DE_genes$b > 0) +up_down_regulated +``` +### Phoretic vs arresting +```{r} +so <- sleuth_prep(dplyr::filter(samples, shortName %in% c("phoretic", "arresting")), target_mapping = t2g,aggregation_column = 'ens_gene', gene_mode = T) +``` + +```{r} +plot_pca(so, color_by = 'condition') +``` + +```{r} +so <- sleuth_fit(so, ~condition, 'full') +so <- sleuth_fit(so, ~1, 'reduced') +so <- sleuth_lrt(so, 'reduced', 'full') +``` + +```{r} +sleuth_table <- sleuth_results(so, 'reduced:full', 'lrt') +sleuth_significant <- dplyr::filter(sleuth_table, qval <= 0.05) +dim(sleuth_significant) +head(sleuth_significant) +``` + +```{r} +models(so) +``` +Number of Differentially expressed genes (TRUE): +```{r} +so = sleuth_wt(so, 'conditionphoretic') +results_table = sleuth_results(so, 'conditionphoretic') +Number_DE_genes = table(results_table$qval <= 0.05) +Number_DE_genes +``` +```{r} +DE_genes = subset(results_table, qval <= 0.05) +DE_genes +up_down_regulated = table(DE_genes$b > 0) +up_down_regulated +``` +### Аrresting vs. pre-laying +```{r} +so <- sleuth_prep(dplyr::filter(samples, shortName %in% c("arresting", "prelaying")), target_mapping = t2g,aggregation_column = 'ens_gene', gene_mode = T) +``` + +```{r} +plot_pca(so, color_by = 'condition') +``` + +```{r} +so <- sleuth_fit(so, ~condition, 'full') +so <- sleuth_fit(so, ~1, 'reduced') +so <- sleuth_lrt(so, 'reduced', 'full') +``` + +```{r} +sleuth_table <- sleuth_results(so, 'reduced:full', 'lrt') +sleuth_significant <- dplyr::filter(sleuth_table, qval <= 0.05) +dim(sleuth_significant) +head(sleuth_significant) +``` + +```{r} +models(so) +``` +Number of Differentially expressed genes (TRUE): +```{r} +so = sleuth_wt(so, 'conditionprelaying') +results_table = sleuth_results(so, 'conditionprelaying') +Number_DE_genes = table(results_table$qval <= 0.05) +Number_DE_genes +``` +```{r} +DE_genes = subset(results_table, qval <= 0.05) +DE_genes +up_down_regulated = table(DE_genes$b > 0) +up_down_regulated +``` +### Pre-laying vs. Laying +```{r} +so <- sleuth_prep(dplyr::filter(samples, shortName %in% c("prelaying", "laying")), target_mapping = t2g,aggregation_column = 'ens_gene', gene_mode = T) +``` + +```{r} +plot_pca(so, color_by = 'condition') +``` + +```{r} +so <- sleuth_fit(so, ~condition, 'full') +so <- sleuth_fit(so, ~1, 'reduced') +so <- sleuth_lrt(so, 'reduced', 'full') +``` + +```{r} +sleuth_table <- sleuth_results(so, 'reduced:full', 'lrt') +sleuth_significant <- dplyr::filter(sleuth_table, qval <= 0.05) +dim(sleuth_significant) +head(sleuth_significant) +``` + +```{r} +models(so) +``` +Number of Differentially expressed genes (TRUE): +```{r} +so = sleuth_wt(so, 'conditionprelaying') +results_table = sleuth_results(so, 'conditionprelaying') +Number_DE_genes = table(results_table$qval <= 0.05) +Number_DE_genes +``` +```{r} +DE_genes = subset(results_table, qval <= 0.05) +DE_genes +up_down_regulated = table(DE_genes$b > 0) +up_down_regulated +``` +### Laying vs. post-laying +```{r} +so <- sleuth_prep(dplyr::filter(samples, shortName %in% c("laying", "postlaying")), target_mapping = t2g,aggregation_column = 'ens_gene', gene_mode = T) +``` + +```{r} +plot_pca(so, color_by = 'condition') +``` + +```{r} +so <- sleuth_fit(so, ~condition, 'full') +so <- sleuth_fit(so, ~1, 'reduced') +so <- sleuth_lrt(so, 'reduced', 'full') +``` + +```{r} +sleuth_table <- sleuth_results(so, 'reduced:full', 'lrt') +sleuth_significant <- dplyr::filter(sleuth_table, qval <= 0.05) +dim(sleuth_significant) +head(sleuth_significant) +``` + +```{r} +models(so) +``` +Number of Differentially expressed genes (TRUE): +```{r} +so = sleuth_wt(so, 'conditionpostlaying') +results_table = sleuth_results(so, 'conditionpostlaying') +Number_DE_genes = table(results_table$qval <= 0.05) +Number_DE_genes +``` +```{r} +DE_genes = subset(results_table, qval <= 0.05) +DE_genes +up_down_regulated = table(DE_genes$b > 0) +up_down_regulated +``` +### Post-laying vs. Emerging +```{r} +so <- sleuth_prep(dplyr::filter(samples, shortName %in% c("postlaying", "emerging")), target_mapping = t2g,aggregation_column = 'ens_gene', gene_mode = T) +``` + +```{r} +plot_pca(so, color_by = 'condition') +``` + +```{r} +so <- sleuth_fit(so, ~condition, 'full') +so <- sleuth_fit(so, ~1, 'reduced') +so <- sleuth_lrt(so, 'reduced', 'full') +``` + +```{r} +sleuth_table <- sleuth_results(so, 'reduced:full', 'lrt') +sleuth_significant <- dplyr::filter(sleuth_table, qval <= 0.05) +dim(sleuth_significant) +head(sleuth_significant) +``` + +```{r} +models(so) +``` +Number of Differentially expressed genes (TRUE): +```{r} +so = sleuth_wt(so, 'conditionpostlaying') +results_table = sleuth_results(so, 'conditionpostlaying') +Number_DE_genes = table(results_table$qval <= 0.05) +Number_DE_genes +``` +```{r} +DE_genes = subset(results_table, qval <= 0.05) +DE_genes +up_down_regulated = table(DE_genes$b > 0) +up_down_regulated +``` +### Post-laying vs. non-laying +```{r} +so <- sleuth_prep(dplyr::filter(samples, shortName %in% c("postlaying", "nonlaying")), target_mapping = t2g,aggregation_column = 'ens_gene', gene_mode = T) +``` + +```{r} +plot_pca(so, color_by = 'condition') +``` + +```{r} +so <- sleuth_fit(so, ~condition, 'full') +so <- sleuth_fit(so, ~1, 'reduced') +so <- sleuth_lrt(so, 'reduced', 'full') +``` + +```{r} +sleuth_table <- sleuth_results(so, 'reduced:full', 'lrt') +sleuth_significant <- dplyr::filter(sleuth_table, qval <= 0.05) +dim(sleuth_significant) +head(sleuth_significant) +``` + +```{r} +models(so) +``` +Number of Differentially expressed genes (TRUE): +```{r} +so = sleuth_wt(so, 'conditionpostlaying') +results_table = sleuth_results(so, 'conditionpostlaying') +Number_DE_genes = table(results_table$qval <= 0.05) +Number_DE_genes +``` +```{r} +DE_genes = subset(results_table, qval <= 0.05) +DE_genes +up_down_regulated = table(DE_genes$b > 0) +up_down_regulated +``` +### Laying vs. non-laying +```{r} +so <- sleuth_prep(dplyr::filter(samples, shortName %in% c("laying", "nonlaying")), target_mapping = t2g,aggregation_column = 'ens_gene', gene_mode = T) +``` + +```{r} +plot_pca(so, color_by = 'condition') +``` + +```{r} +so <- sleuth_fit(so, ~condition, 'full') +so <- sleuth_fit(so, ~1, 'reduced') +so <- sleuth_lrt(so, 'reduced', 'full') +``` + +```{r} +sleuth_table <- sleuth_results(so, 'reduced:full', 'lrt') +sleuth_significant <- dplyr::filter(sleuth_table, qval <= 0.05) +dim(sleuth_significant) +head(sleuth_significant) +``` + +```{r} +models(so) +``` +Number of Differentially expressed genes (TRUE): +```{r} +so = sleuth_wt(so, 'conditionnonlaying') +results_table = sleuth_results(so, 'conditionnonlaying') +Number_DE_genes = table(results_table$qval <= 0.05) +Number_DE_genes +``` +```{r} +DE_genes = subset(results_table, qval <= 0.05) +DE_genes +up_down_regulated = table(DE_genes$b > 0) +up_down_regulated +``` +### Emerging vs. Phoretic +```{r} +so <- sleuth_prep(dplyr::filter(samples, shortName %in% c("emerging", "phoretic")), target_mapping = t2g,aggregation_column = 'ens_gene', gene_mode = T) +``` + +```{r} +plot_pca(so, color_by = 'condition') +``` + +```{r} +so <- sleuth_fit(so, ~condition, 'full') +so <- sleuth_fit(so, ~1, 'reduced') +so <- sleuth_lrt(so, 'reduced', 'full') +``` + +```{r} +sleuth_table <- sleuth_results(so, 'reduced:full', 'lrt') +sleuth_significant <- dplyr::filter(sleuth_table, qval <= 0.05) +dim(sleuth_significant) +head(sleuth_significant) +``` + +```{r} +models(so) +``` +Number of Differentially expressed genes (TRUE): +```{r} +so = sleuth_wt(so, 'conditionphoretic') +results_table = sleuth_results(so, 'conditionphoretic') +Number_DE_genes = table(results_table$qval <= 0.05) +Number_DE_genes +``` +```{r} +DE_genes = subset(results_table, qval <= 0.05) +DE_genes +up_down_regulated = table(DE_genes$b > 0) +up_down_regulated +``` +### Emerging vs. Young +```{r} +so <- sleuth_prep(dplyr::filter(samples, shortName %in% c("emerging", "young")), target_mapping = t2g,aggregation_column = 'ens_gene', gene_mode = T) +``` + +```{r} +plot_pca(so, color_by = 'condition') +``` + +```{r} +so <- sleuth_fit(so, ~condition, 'full') +so <- sleuth_fit(so, ~1, 'reduced') +so <- sleuth_lrt(so, 'reduced', 'full') +``` + +```{r} +sleuth_table <- sleuth_results(so, 'reduced:full', 'lrt') +sleuth_significant <- dplyr::filter(sleuth_table, qval <= 0.05) +dim(sleuth_significant) +head(sleuth_significant) +``` + +```{r} +models(so) +``` +Number of Differentially expressed genes (TRUE): +```{r} +so = sleuth_wt(so, 'conditionyoung') +results_table = sleuth_results(so, 'conditionyoung') +Number_DE_genes = table(results_table$qval <= 0.05) +Number_DE_genes +``` +```{r} +DE_genes = subset(results_table, qval <= 0.05) +DE_genes +up_down_regulated = table(DE_genes$b > 0) +up_down_regulated +``` \ No newline at end of file diff --git a/genebank_gene_map.csv b/genebank_gene_map.csv new file mode 100644 index 0000000..be19730 --- /dev/null +++ b/genebank_gene_map.csv @@ -0,0 +1,30209 @@ +ens_gene,target_id +LOC111248800,XM_022801782.1 +LOC111248800,XM_022801763.1 +LOC111248800,XM_022801774.1 +LOC111248800,XM_022801754.1 +LOC111255390,XM_022817320.1 +LOC111255390,XM_022817318.1 +LOC111255390,XM_022817319.1 +LOC111249091,XM_022802455.1 +LOC111255382,XM_022817303.1 +LOC111255382,XM_022817300.1 +LOC111255382,XM_022817302.1 +LOC111255382,XM_022817301.1 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