quick_lm: Perform single marker regression tests.
In amkusmec/FarmCPUpp: Perform GWAS Using the FarmCPU Model

Description Usage Arguments Value Author(s)

Returns single marker regression test results for all markers in GDP, effect estimates for covariates (user-specified and pseudo-QTNs), and p-values for pseudo-QTNs used by get_qtns.

1	quick_lm(Y = NULL, GDP = NULL, CV = NULL, npc = 0, seqQTN = NULL)

`Y`	A numeric vector of phenotype values. May include missing values.
`GDP`	A pointer to a big.matrix object.
`CV`	A numeric matrix where each column contains values for a covariate.
`npc`	An integer scalar. Number of columns of `CV` that contain user-defined covariates.
`seqQTN`	An integer vector denoting the column in `GDP` of each pseudo-QTN.

A list containing the following components:

P: a numeric matrix whose first four columns contain the effect estimate, standard error, t statistic, and p-value for each single marker regression test. Subsequent columns contain p-values for pseudo-QTNs when used as a covariate when testing each marker.
P0: a numeric vector containing p-values for the mean, user-specified covariates, and pseudo-QTNs in the null model.
betapc: a numeric vector of effect estimates for user-specified covariates.

Aaron Kusmec

amkusmec/FarmCPUpp documentation built on Dec. 25, 2021, 10:05 p.m.