sqtls: sQTLs retrieval
In jmonlong/sQTLseekeR: Splicing QTL discovery tool

Description Usage Arguments Details Value Author(s)

Retrieves sQTLs after multiple testing correction and potentially removing svQTLs. The distribution of the P-values and a semi-volcano plot can also be shown.

1 2	sqtls(res.df, FDR = 0.01, md.min = 0.01, out.pdf = NULL, svQTL.removal = TRUE, FDR.svQTL = 0.01)

`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 0.01.
`md.min`	the minimum MD (Maximum Difference) in relative expression desired. Maximum difference in relative expression (MD) gives an idea of the effect size of the association. Default is 0.01.
`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 possibly removed from the final set of sQTLs.

Multiple testing correction is performed using qvalue package with default parameters.

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

jmonlong/sQTLseekeR documentation built on May 19, 2019, 1:54 p.m.