README.md

In clinico-omics/exp2qcdt: Convert expression table to qc datatable for quartet project

EXP2QCDT

Convert expression table to qc data table for quartet project.

Installation

devtools::install_github("clinico-omics/exp2qcdt")

Usage

library(exp2qcdt)
exp2qcdt("~/Downloads/exp2qcdt/test/fpkm_table.txt", "~/Downloads/exp2qcdt/test/counts_table.txt", "~/Downloads/exp2qcdt/test/phenotype.txt", "~/Downloads/exp2qcdt/test/")

phenotype 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 |

fpkm 和 counts library ID 需要和 photype 要完全一致

reference data

1.refqc_202011_forplot.rds 记录了 21 批次参考数据，6 种组合(D6/D5, F7/D5, M8/D5, F7/D6, M8/D6, M8/F7) relative correlation 值，以及 6 种组合参考数据集 logfc 之间的相关性，总共就是 21X6 行。第 4 列 corr_ref (Reference datasets based relative correlation) 就是参考数据集 logfc 之间的相关性，第 6 列 corr_FC (Relative correlation) 就是

Reference datasets based relative correlation 解释 比如说：D6/D5，所有基因有一个 logfc，然后 D6/D5 与 21 个 batch D6/D5 logfc 做相关性，结果就是新的数据集 D6/D5 logfc 与参考数据之间的 logfc 相关性 relative correlation 的解释 比如说：D6/D5，1. 三个 replicate 之间就有（D6_1/D5_1, D6_2/D5_1, D6_3/D5_1, D6_1/D5_2, D6_2/D5_2, D6_3/D5_2, D6_1/D5_3, D6_2/D5_3, D6_3/D5_3）9 种相对表达值；2. 9 种相对表达两两 correlation，就有了 36 个 correlation，然后取均值，就是每一个 batch，D6/D5 的 relative correlation

1. TableS2_ReferenceDatasets.csv

   6 种组合(D6/D5, F7/D5, M8/D5, F7/D6, M8/D6, M8/F7)，11797 个基因 logfc 的均值。

Contributors

• Jun Shang
• Jingcheng Yang

clinico-omics/exp2qcdt documentation built on June 11, 2021, 1:44 p.m.