sqtls.p: sQTL retrieval from permuted phenotypes
In dgarrimar/sQTLseekeR2: R package for splicing QTL mapping

Description Usage Arguments Details Value Author(s)

Retrieves sQTLs after two-level multiple testing correction and svQTL removal (if requested).

sqtls.p(
  res.nominal.df,
  res.permuted.df,
  FDR = 0.05,
  method = "BH",
  md.min = 0.05,
  svQTL.removal = FALSE,
  FDR.svQTL = 0.05
)

`res.nominal.df`	a data.frame, output of 'sqtl.seeker' with the nominal P-values for each gene/SNP test.
`res.permuted.df`	a data.frame, output of 'sqtl.seeker.p' with the empirical P-values and the MLE estimates for the beta distribution parameters for each gene.
`FDR`	the False Discovery Rate to call an association significant. Default is 0.05.
`method`	the FDR approach. Either `"BH"` (Benjamini-Hochberg) or `"qvalue"` (Storey). The latter tends to be less stringent. Default is "BH".
`md.min`	the minimum MD (Maximum Difference) in relative expression required. Maximum difference in relative expression (MD) gives an idea of the effect size of the association. Default is 0.05.
`svQTL.removal`	if TRUE (and column 'pv.svQTL' is present in 'res.df') significant sQTL which are also significant svQTLs are not reported. Default is FALSE.
`FDR.svQTL`	the False Discovery Rate to call a svQTL, that may be removed from the final set of sQTLs. Note that svQTL FDR is computed on the pooled nominal P-values from the svQTL test.

We consider two levels of multiple testing:

1. Multiple genetic variants are tested per gene.
2. Multiple genes are tested genome-wide.

sQTLseekeR2 uses a permutation approach, implemented and detailed in sqtl.seeker.p to correct for the former and false discovery rate (FDR) estimation to control for the latter. Both Benjamini-Hochberg (p.adjust method) and Storey (qvalue method) approaches for FDR can be applied.

If svQTL.removal = TRUE and svQTLs were tested in 'sqtl.seeker', gene/SNPs with significant svQTL association (after multiple testing correction and similar FDR threshold) are removed from the final set of significant sQTLs.

a data.frame with the columns of sqtl.seeker and sqtl.seeker.p outputs with the significant sQTLs.

Diego Garrido-Martín

dgarrimar/sQTLseekeR2 documentation built on Nov. 22, 2021, 3:23 a.m.