This repository contains custom R scripts for performing RNA-seq differential gene expression analysis, along with scripts for generating PCA plots and boxplots of expression data.
Help:
Usage: differential_expression.R [options]
Example: Rscript differential_expression.R -r rnaseq_results -d 'DEG' -t 'Malignant' -c 'Benign' --batch_effect TRUE --norm_counts TRUE --alpha 0.05
Options:
-d STRING, --differential_expression=STRING
Type of differential expression to perform. DEG for Differentially expressed genes. DET for differential expressed transcripts. DEM for differential expression miRNAseq
-e BOOLEAN, --deseq2=BOOLEAN
Perform DESeq2 DE or not.
-f BOOLEAN, --fishpond=BOOLEAN
Perform fishpond DE or not.
-r PATH, --rnaseq_dir=PATH
Path to rna-seq results
-s PATH, --sample_data=PATH
Path to clinical data file
-g STRING, --group_col=STRING
Colname with the sample classes in sample_data of the experiment for the DE.
-i STRING, --batch_col=STRING
Colname of the column with the batch information.
-a INTEGER, --alpha=INTEGER
Alpha value to filter genes by p-value before BH correction in padj. Must be between 1 and 0
-t STRING, --treatment=STRING
Treatment group name.
-c STRING, --control=STRING
Control group name.
-b BOOLEAN, --batch_effect=BOOLEAN
Correct by batch effect
-n BOOLEAN, --norm_counts=BOOLEAN
Create table with normalized counts
-q BOOLEAN, --quality_plots=BOOLEAN
Create quality plots or not.
-k BOOLEAN, --multiple_groups=BOOLEAN
Perform multiple groups or not. Eg: Group (A+B) vs Group C
-h, --help
Show this help message and exitHelp:
Usage: custom_pca.R [options]
Example: Rscript custom_pca.R -r Malignant_Benign/.RData -o Malignant_Benign/PCA.tiff -f FALSE
Options:
-r PATH, --rdata_dir=PATH
Path to differential expression history
-o PATH, --out_tiff=PATH
Output file path/name to save tiff image
-g BOOLEAN, --group_samples=BOOLEAN
Whether group samples in the plot or not.
-h, --help
Show this help message and exitHelp:
Usage: custom_boxplot.R [options]
Example: Rscript custom_boxplot.R --rdata_dir ./.RData --tpm_data ./salmon.merged.gene_tpm.tsv --log_transform TRUE
Options:
-r PATH, --rdata_dir=PATH
Path to differential expression history to perform boxplots from DESeq2 normalized counts. Default: NULL to perform only with TPM data.
-t PATH, --tpm_data=PATH
Path to TPM expression data to perform boxplots from TPM expression. Default: NULL to perform only with DESeq norm counts data.
-l BOOLEAN, --log_transform=BOOLEAN
Wheter to perform logarithmic transformation of the TPM data
-o PATH, --out_folder=PATH
Output folder to save tiff images. Default: './box_plot'
-g PATH, --gene_list=PATH
Path to the list of genes that are going to be plotted. Default: './gene_list.txt'
-m PATH, --metadata=PATH
Path to the metadata with groups for colouring. Default: './clinical_data.txt'
-h, --help
Show this help message and exitHelp:
Usage: heatmap.R [options]
Example: Rscript heatmap.R --norm_counts ./norm_counts.tsv --tpm_data ./salmon.merged.gene_tpm.tsv --log_transform TRUE
Options:
-r PATH, --norm_counts=PATH
Path to normalized expression table.
-t PATH, --tpm_data=PATH
Path to TPM expression data to perform boxplots from TPM expression. Default: NULL to perform only with DESeq norm counts data.
-l BOOLEAN, --log_transform=BOOLEAN
Wheter to perform logarithmic transformation of the TPM data
-o PATH, --out_folder=PATH
Output folder to save tiff images. Default: './box_plot'
-g PATH, --gene_list=PATH
Path to the list of genes that are going to be plotted. Default: './gene_list.txt'
-m PATH, --metadata=PATH
Path to the metadata with groups for colouring. Default: './clinical_data.txt'
-h, --help
Show this help message and exit