BM_project_exp_4_H3K27ac

Libraries

library(tidyverse)
library(plotly)
library(car)
library(rstatix)
library(SimComp)
library(readxl)

Datasets

dataset_exp_4_h3k27ac <- read_excel (path = "/mnt/c/Users/Toshiya Matsushima/OneDrive/R projects/BM_project/data analysis using Rstudio/BM_project_dataset.xlsx", sheet = "exp_4_h3k27ac")
dataset_exp_4_h3k27ac

Figure

fig <- ggplot(data = dataset_exp_4_h3k27ac, mapping = aes(x=drug, y=flu)) +
  geom_beeswarm(size = 1, shape = 16, colour = "black") +
  theme_classic()
fig
ggsave(plot = fig, filename = "exp_4_h3k27ac.png", dpi = 300, height = 10, width = 10, units = "cm")

Analysis

ANOVA (one-way)

dataset_exp_4_h3k27ac %>%
  anova_test(flu ~ drug)

Coefficient covariances computed by hccm()

ANOVA Table (type II tests)

  Effect DFn DFd       F         p p<.05 ges
1   drug   4 495 288.695 6.97e-128     * 0.7

Linear fitting analysis

fit_exp_4_h3k27ac <- lm(flu ~ drug, data = dataset_exp_4_h3k27ac)
summary(fit_exp_4_h3k27ac)

Call:
lm(formula = flu ~ drug, data = dataset_exp_4_h3k27ac)

Residuals:
    Min      1Q  Median      3Q     Max 
-9.9914 -1.7085 -0.3416  1.0087 27.7386 

Coefficients:
                   Estimate Std. Error t value Pr(>|t|)    
(Intercept)          7.4293     0.3156  23.537   <2e-16 ***
drug01_VPA_0_low     0.5917     0.4464   1.326    0.186    
drug01_vpa_1_high   11.9921     0.4464  26.865   <2e-16 ***
drug02_keta_0_low   -0.4920     0.4464  -1.102    0.271    
drug02_keta_1_high   0.0230     0.4464   0.052    0.959    
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Residual standard error: 3.156 on 495 degrees of freedom
Multiple R-squared:    0.7, Adjusted R-squared:  0.6975 
F-statistic: 288.7 on 4 and 495 DF,  p-value: < 2.2e-16

car::Anova(fit_exp_4_h3k27ac)

Anova Table (Type II tests)

Response: flu
           Sum Sq  Df F value    Pr(>F)    
drug      11504.9   4   288.7 < 2.2e-16 ***
Residuals  4931.6 495                      
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

sessionInfo

sessionInfo()

R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8        LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8   
 [6] LC_MESSAGES=C.UTF-8    LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C           LC_TELEPHONE=C        
[11] LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] ggsci_2.9        pwr_1.3-0        plotly_4.10.0    readxl_1.3.1     SimComp_3.3      rstatix_0.7.0    car_3.0-12      
 [8] carData_3.0-5    plotrix_3.8-2    ggbeeswarm_0.6.0 forcats_0.5.1    stringr_1.4.0    dplyr_1.0.7      purrr_0.3.4     
[15] readr_2.1.1      tidyr_1.1.4      tibble_3.1.6     ggplot2_3.3.5    tidyverse_1.3.1 

loaded via a namespace (and not attached):
 [1] nlme_3.1-144         fs_1.5.2             lubridate_1.8.0      httr_1.4.2           tools_3.6.3          backports_1.4.1     
 [7] utf8_1.2.2           R6_2.5.1             vipor_0.4.5          mgcv_1.8-31          DBI_1.1.1            lazyeval_0.2.2      
[13] colorspace_2.0-2     withr_2.4.3          tidyselect_1.1.1     compiler_3.6.3       survPresmooth_1.1-11 mratios_1.4.2       
[19] cli_3.1.0            rvest_1.0.2          xml2_1.3.3           sandwich_3.0-1       labeling_0.4.2       scales_1.1.1        
[25] mvtnorm_1.1-3        digest_0.6.29        rmarkdown_2.11       pkgconfig_2.0.3      htmltools_0.5.2      dbplyr_2.1.1        
[31] fastmap_1.1.0        htmlwidgets_1.5.4    rlang_0.4.12         rstudioapi_0.13      jquerylib_0.1.4      generics_0.1.1      
[37] farver_2.1.0         zoo_1.8-9            jsonlite_1.7.2       magrittr_2.0.1       Matrix_1.2-18        Rcpp_1.0.7          
[43] munsell_0.5.0        fansi_0.5.0          abind_1.4-5          lifecycle_1.0.1      stringi_1.7.6        multcomp_1.4-18     
[49] yaml_2.2.1           MASS_7.3-51.5        grid_3.6.3           crayon_1.4.2         lattice_0.20-40      haven_2.4.3         
[55] splines_3.6.3        hms_1.1.1            knitr_1.37           pillar_1.6.4         codetools_0.2-16     reprex_2.0.1        
[61] glue_1.6.0           evaluate_0.14        data.table_1.14.2    modelr_0.1.8         vctrs_0.3.8          tzdb_0.2.0          
[67] cellranger_1.1.0     gtable_0.3.0         assertthat_0.2.1     xfun_0.29            broom_0.7.10         survival_3.1-8      
[73] viridisLite_0.4.0    beeswarm_0.4.0       TH.data_1.1-0        ellipsis_0.3.2