Convert expression table to qc data table for quartet project.
devtools::install_github("chinese-quartet/quartet-rseqc-report", subdir = "exp2qcdt")library(exp2qcdt)
exp2qcdt("~/Downloads/exp2qcdt/test/fpkm_table.txt", "~/Downloads/exp2qcdt/test/counts_table.txt", "~/Downloads/exp2qcdt/test/phenotype.txt", "~/Downloads/exp2qcdt/test/")| 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 phenotype
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.