EXP2QCDT

Guideline for Quartet RNA QC Pipeline. The exp2qcdt package aims to convert expression table to qc data table for quartet project.

Installation

## If you do not have devtools, please install first
library(devtools)
devtools::install_github("chinese-quartet/Quartet-RNA-QC-report", subdir = "exp2qcdt")

Usage

library(exp2qcdt)

## please prepare your input file in the following format. (Make sure the column names are the same format with the examples)

RNA_sample_fpkm <- system.file("extdata","fpkm.csv",package = "exp2qcdt")
RNA_sample_count <- system.file("extdata","count.csv",package = "exp2qcdt")
RNA_sample_metadata <- system.file("extdata","metadata.csv",package = "exp2qcdt")

# RNA_result = exp2qcdt("~/Downloads/exp2qcdt/test/fpkm_table.txt", "~/Downloads/exp2qcdt/test/counts_table.txt", "~/Downloads/exp2qcdt/test/phenotype.txt", "~/Downloads/exp2qcdt/test/")
RNA_result <- exp2qcdt(exp_table_file = RNA_sample_fpkm,count_table_file = RNA_sample_count,phenotype_file = RNA_sample_metadata,result_dir = "./RNA_output/")
## Get QC report template file path 
RNA_doc_temp <- system.file("extdata","Quartet_temp.docx",package = "exp2qcdt")

##  Generate QC report
GenerateRNAReport(RNA_result = RNA_result,doc_file_path = RNA_doc_temp,output_path = "./RNA_output/")

metadata table example

library	group	sample
Quartet_RNA_BGI_BGI2000_PolyA_BGI_D5_1_20200618	D5_1	D5
Quartet_RNA_BGI_BGI2000_PolyA_BGI_D5_2_20200618	D5_2	D5
Quartet_RNA_BGI_BGI2000_PolyA_BGI_D5_3_20200618	D5_3	D5
Quartet_RNA_BGI_BGI2000_PolyA_BGI_D6_1_20200618	D6_1	D6
Quartet_RNA_BGI_BGI2000_PolyA_BGI_D6_2_20200618	D6_2	D6
Quartet_RNA_BGI_BGI2000_PolyA_BGI_D6_3_20200618	D6_3	D6
Quartet_RNA_BGI_BGI2000_PolyA_BGI_F7_1_20200618	F7_1	F7
Quartet_RNA_BGI_BGI2000_PolyA_BGI_F7_2_20200618	F7_2	F7
Quartet_RNA_BGI_BGI2000_PolyA_BGI_F7_3_20200618	F7_3	F7
Quartet_RNA_BGI_BGI2000_PolyA_BGI_M8_1_20200618	M8_1	M8
Quartet_RNA_BGI_BGI2000_PolyA_BGI_M8_2_20200618	M8_2	M8
Quartet_RNA_BGI_BGI2000_PolyA_BGI_M8_3_20200618	M8_3	M8

The fpkm and counts library IDs need to be identical to metadata

reference data

ref_data_fc_value.csv The log2fc of D5/D6, F7/D6, M8/D6 were calculated for the filtered genes based on the reference dataset.

ref_data_qc_value.csv SNR, RC, Total Score value of 21 historical datasets.

Contributors

• Jun Shang
• Jingcheng Yang