dpt_test: dpt_test

In ScialdoneLab/MitoHEAR: Quantification of Mitochondrial DNA Heteroplasmy

dpt_test

Description

dpt_test

Usage

dpt_test(heteroplasmy_matrix, time, index = NULL, method = "GAM")

Arguments

heteroplasmy_matrix	Third element returned by get_heteroplasmy.
time	Vector of diffusion pseudo time.
index	index returned by get_heteroplasmy.
method	Character name denoting the method to choose for assigning an adjusted p value to each of the bases. Can be one of GAM, pearson and spearman. GAM: For each base, a GAM fit with formula z ~ lo(t) is performed between the heteroplasmy values (z) and the time (t). The p value from the table "Anova for Parametric Effects" is then assigned to the base. pearson,spearman:for each base, a pearson or spearman correlation test is performed between the heteroplasmy values and the time . The p value obtained from the test is then assigned to the base. In all the three possible methods, all the p values are then corrected with the method FDR.

Value

A data frame with 2 columns and number of rows equal to n_col in heteroplasmy_matrix. In the first column there are the names of the bases while in the second column there are the adjusted p value.

Author(s)

Gabriele Lubatti [e-mail]

See Also

https://www.rdocumentation.org/packages/gam/versions/1.20/topics/gam

ScialdoneLab/MitoHEAR documentation built on June 11, 2022, 7:18 a.m.