README.md

In chinese-quartet/ProtQC: ProtQC

ProtQC

Description

The package ProtQC visualizes Quality Control(QC) results for Quartet Project.

Required Packages

dplyr,data.table,ggplot2,ggthemes,edgeR,limma

Installation

devtools::install_github("chinese-quartet/ProtQC")

Usage

ProtQC::plot_pca(expr_dt_path,meta_dt_path,output_dir)

ProtQC::plot_corr(expr_dt_path,meta_dt_path,output_dir)

ProtQC::table_conclusion(expr_dt_path,meta_dt_path,output_dir)

Examples

ProtQC::plot_pca('./data/test_data_example.csv','./data/test_metadata_example.csv','~/Desktop/')

ProtQC::plot_corr('./data/test_data_example.csv','./data/test_metadata_example.csv','~/Desktop/')

ProtQC::table_conclusion('./data/test_data_example.csv','./data/test_metadata_example.csv','~/Desktop/')

Built-in Dataset

1. example_ref_dt.rds

This file is an example for reference data set, which is a benchmarked proteomics profiled data set for Quality Control.

1. ref_snrcorr.rds

This file is used in ranking scores of the testing data set in the historical values.

Examples for the input data

1. data/input/test_data_example.csv

This file is an example for proteomics profiled data (expr_dt, one of the input parameters for these functions: plot_pca(), plot_corr(),table_conclusion()), containing gene symbols of each protein and its quantitated expression level in each sample (replicate), and the missing values are replaced by NA.

1. data/input/test_metadata_example.csv

This file is an example for proteomics metadata (meta_dt, one of the input parameters for these functions: plot_pca(), plot_corr(),table_conclusion()).

Here is a quick view:

| name | sample | | :----------------------------- | ------ | | B1_DDA_JNU_Lumos_Firmiana_D5_1 | D5 | | B1_DDA_JNU_Lumos_Firmiana_D5_2 | D5 | | B1_DDA_JNU_Lumos_Firmiana_D5_3 | D5 | | B1_DDA_JNU_Lumos_Firmiana_D6_1 | D6 | | B1_DDA_JNU_Lumos_Firmiana_D6_2 | D6 | | B1_DDA_JNU_Lumos_Firmiana_D6_3 | D6 | | B1_DDA_JNU_Lumos_Firmiana_F7_1 | F7 | | B1_DDA_JNU_Lumos_Firmiana_F7_2 | F7 | | B1_DDA_JNU_Lumos_Firmiana_F7_3 | F7 | | B1_DDA_JNU_Lumos_Firmiana_M8_1 | M8 | | B1_DDA_JNU_Lumos_Firmiana_M8_2 | M8 | | B1_DDA_JNU_Lumos_Firmiana_M8_3 | M8 |

Note: The column names of expr_dt and meta_dt$name must be in one-to-one correspondence.

chinese-quartet/ProtQC documentation built on Dec. 19, 2021, 3:57 p.m.