sqtls: sQTL retrieval
In guigolab/sQTLseekeR2: R package for splicing QTL mapping

Description Usage Arguments Details Value Author(s)

Retrieves sQTLs after multiple testing correction and svQTL removal (if requested). The distribution of the P-values and a semi-volcano plot can be also displayed.

sqtls(
  res.df,
  FDR = 0.05,
  method = "BH",
  md.min = 0.05,
  out.pdf = NULL,
  svQTL.removal = TRUE,
  FDR.svQTL = 0.05
)

`res.df`	a data.frame, output of 'sqtl.seeker' with the P-values for each gene/SNP test.
`FDR`	the False Discovery Rate to call an association significant. Default is 0.05.
`method`	FDR approach: either `"BH"` (Benjamini-Hochberg) or `"qvalue"` (Storey). Default is "BH".
`md.min`	the minimum MD (Maximum Difference) in relative expression. Maximum difference in relative expression (MD) gives an idea of the effect size of the association. Default is 0.05.
`out.pdf`	the name of the pdf file to create. If NULL (default), no pdf output will be created. If non-NULL, the distribution of the P-values and a semi-volcano plot (P-value vs MD) will be shown.
`svQTL.removal`	if TRUE (and column 'pv.svQTL' is present in 'res.df') significant sQTL which are also significant svQTLs are not reported.
`FDR.svQTL`	the False Discovery Rate to call a svQTL, that may be removed from the final set of sQTLs.

Multiple testing correction can be performed using either Benjamini-Hochberg (p.adjust method) or Storey (qvalue method) approach for FDR.

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 subset of the input data.frame with only significant sQTLs and FDR estimates.

Jean Monlong, Diego Garrido-Martín

guigolab/sQTLseekeR2 documentation built on Nov. 20, 2021, 3:21 a.m.