run_estimation {CB2} | R Documentation |

## A function to perform a statistical test at a sgRNA-level, deprecated.

### Description

A function to perform a statistical test at a sgRNA-level, deprecated.

### Usage

```
run_estimation(
sgcount,
design,
group_a,
group_b,
delim = "_",
ge_id = NULL,
sg_id = NULL
)
```

### Arguments

`sgcount` |
This data frame contains read counts of sgRNAs for the samples. |

`design` |
This table contains study design. It has to contain 'group.' |

`group_a` |
The first group to be tested. |

`group_b` |
The second group to be tested. |

`delim` |
The delimiter between a gene name and a sgRNA ID. It will be used if only rownames contains sgRNA ID. |

`ge_id` |
The column name of the gene column. |

`sg_id` |
The column/columns of sgRNA identifiers. |

### Value

A table contains the sgRNA-level test result, and the table contains these columns:

‘sgRNA’: The sgRNA identifier.

‘gene’: The gene is the target of the sgRNA

‘n_a’: The number of replicates of the first group.

‘n_b’: The number of replicates of the second group.

‘phat_a’: The proportion value of the sgRNA for the first group.

‘phat_b’: The proportion value of the sgRNA for the second group.

‘vhat_a’: The variance of the sgRNA for the first group.

‘vhat_b’: The variance of the sgRNA for the second group.

‘cpm_a’: The mean CPM of the sgRNA within the first group.

‘cpm_b’: The mean CPM of the sgRNA within the second group.

‘logFC’: The log fold change of sgRNA between two groups.

‘t_value’: The value for the t-statistics.

‘df’: The value of the degree of freedom, and will be used to calculate the p-value of the sgRNA.

‘p_ts’: The p-value indicates a difference between the two groups.

‘p_pa’: The p-value indicates enrichment of the first group.

‘p_pb’: The p-value indicates enrichment of the second group.

‘fdr_ts’: The adjusted P-value of ‘p_ts’.

‘fdr_pa’: The adjusted P-value of ‘p_pa’.

‘fdr_pb’: The adjusted P-value of ‘p_pb’.

*CB2*version 1.3.4 Index]