View source: R/automated_RNAseq_analysis.R
AutoExtraction | R Documentation |
Automated extraction of gene set from count matrix and plot by boxplot
AutoExtraction(Count_matrix, Gene_set_dir)
Count_matrix |
count matrix txt file |
Gene_set_dir |
Directory including gene set txt files |
Hadley Wickham, Romain François, Lionel Henry and Kirill Müller (2021). dplyr: A Grammar of Data Manipulation. R package version 1.0.7. https://CRAN.R-project.org/package=dplyr
Hadley Wickham (2021). tidyr: Tidy Messy Data. R package version 1.1.3. https://CRAN.R-project.org/package=tidyr
R. Gentleman, V. Carey, W. Huber and F. Hahne (2021). genefilter: methods for filtering genes from high-throughput experiments. R package version 1.72.1.
Gu, Z. (2016) Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics.
H. Wickham. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York, 2016.
Alboukadel Kassambara (2020). ggpubr: 'ggplot2' Based Publication Ready Plots. R package version 0.4.0. https://CRAN.R-project.org/package=ggpubr
library(rnaseqviewer) data(DEG_list) dir.create("DEG_list") write.table(DEG_list[1], file = "DEG_list/dataset1.txt", sep = "\t", quote = FALSE) write.table(DEG_list[2], file = "DEG_list/dataset2.txt", sep = "\t", quote = FALSE) vennd("DEG_list") data(Row_count_3conditions) write.table(Row_count_3conditions, file = "Row_count_3conditions.txt", sep = "\t", quote = FALSE) AutoExtraction(Count_matrix = "Row_count_3conditions.txt", Gene_set_dir = "DEG_list/group_lists")
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