GSAQ: Gene Set Analysis with QTL

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Computation of Quantitative Trait Loci hits in the selected gene set. Performing gene set validation with Quantitative Trait Loci information. Performing gene set enrichment analysis with available Quantitative Trait Loci data and computation of statistical significance value from gene set analysis. Obtaining the list of Quantitative Trait Loci hit genes along with their overlapped Quantitative Trait Loci names.

Author
Samarendra Das <samarendra.das@icar.gov.in>
Date of publication
2016-09-08 13:07:11
Maintainer
Samarendra Das <samarendra.das@icar.gov.in>
License
GPL (>= 2)
Version
1.0

View on CRAN

Man pages

genedist
Chromosomal distribution of the genes in the selected geneset
genelist
A list of genes of rice
geneqtl
List of the selected genes along with their corresponding...
GeneSelect
Selection of informative geneset
GSAQ
Gene Set Analysis with Quantitative Trait Loci with gene...
GSVQ
Gene Set Validation with QTL using Hyper-geometric test...
qtldist
QTL wise distribution of genes in the selected geneset
qtlhit
Computation of qtl-hit statistic for the selected gene set
qtl_salt
A list of salt responsive Quantitative Trait Loci of rice
rice_salt
Gene expression data of rice under salinity stress
totqtlhit
Computation of total number of qtl-hits found in the whole...

Files in this package

GSAQ
GSAQ/NAMESPACE
GSAQ/data
GSAQ/data/qtl_salt.rda
GSAQ/data/genelist.rda
GSAQ/data/rice_salt.rda
GSAQ/R
GSAQ/R/GSAQ.R
GSAQ/MD5
GSAQ/DESCRIPTION
GSAQ/man
GSAQ/man/qtl_salt.Rd
GSAQ/man/rice_salt.Rd
GSAQ/man/GeneSelect.Rd
GSAQ/man/geneqtl.Rd
GSAQ/man/GSVQ.Rd
GSAQ/man/qtldist.Rd
GSAQ/man/genelist.Rd
GSAQ/man/qtlhit.Rd
GSAQ/man/totqtlhit.Rd
GSAQ/man/genedist.Rd
GSAQ/man/GSAQ.Rd