sqtls: sQTL retrieval

Description Usage Arguments Details Value Author(s)

View source: R/sqtls.R

Description

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.

Usage

1
2
3
4
5
6
7
8
9
sqtls(
  res.df,
  FDR = 0.05,
  method = "BH",
  md.min = 0.05,
  out.pdf = NULL,
  svQTL.removal = TRUE,
  FDR.svQTL = 0.05
)

Arguments

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.

Details

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.

Value

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

Author(s)

Jean Monlong, Diego Garrido-Martín


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