View source: R/calculate_pvalue.R

calculate_pvalue | R Documentation |

Displays stars for each cell type corresponding to the significance level of two mean comparison tests between expression levels (high or low) with multiple correction.

```
calculate_pvalue(
x,
method_test = "wilcox_test",
method_adjust = "BH",
p_threshold = 0.05
)
```

`x` |
object from |

`method_test` |
character for the choice of the statistical test among 't_test' or 'wilcox_test'. |

`method_adjust` |
character for the choice of the multiple correction test among 'BH', 'bonferroni', 'BY', 'fdr', 'hochberg', 'holm', 'hommel', 'none' |

`p_threshold` |
float for the significativity threshold of the P-value. |

rstatix_test object for a table with cell types in the row and P-values, corrections and other statistics in the column.

```
data(tcga)
(df <- convert2biodata(
algorithm = "Cibersort_ABS",
disease = "breast invasive carcinoma",
tissue = "Primary Tumor",
gene_x = "ICOS"
))
calculate_pvalue(df)
calculate_pvalue(
df,
method_test = "t_test",
method_adjust = "bonferroni",
p_threshold = 0.01
)
```

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