norm.fact {rCNV} | R Documentation |
Calculate normalization factor for each sample
Description
This function calculates the normalization factor for each sample using different methods. See details.
Usage
norm.fact(
df,
method = c("TMM", "TMMex", "MedR", "QN"),
logratioTrim = 0.3,
sumTrim = 0.05,
Weighting = TRUE,
Acutoff = -1e+10
)
Arguments
df |
a data frame or matrix of allele depth values (total depth per snp per sample) |
method |
character. method to be used (see details). Default |
logratioTrim |
numeric. percentage value (0 - 1) of variation to be trimmed in log transformation |
sumTrim |
numeric. amount of trim to use on the combined absolute
levels (“A” values) for method |
Weighting |
logical, whether to compute (asymptotic binomial precision) weights |
Acutoff |
numeric, cutoff on “A” values to use before trimming |
Details
Originally described for normalization of RNA sequences
(Robinson & Oshlack 2010), this function computes normalization (scaling)
factors to convert observed library sizes into effective library sizes.
It uses the method trimmed means of M-values proposed by Robinson &
Oshlack (2010). See the original publication and edgeR
package
for more information.
The method MedR
is median ratio normalization;
QN - quantile normalization (see Maza, Elie, et al. 2013 for a
comparison of methods).
Value
Returns a numerical vector of normalization factors for each sample
Author(s)
Piyal Karunarathne
References
Robinson MD, and Oshlack A (2010). A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biology 11, R25
Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26
Examples
vcf.file.path <- paste0(path.package("rCNV"), "/example.raw.vcf.gz")
vcf <- readVCF(vcf.file.path)
df<-hetTgen(vcf,"AD-tot",verbose=FALSE)
norm.fact(df)