getDSPatterns {maSigPro} | R Documentation |
getDSPatterns
is a function that makes a list with the names of genes identified with tableDS
function.
getDSPatterns(tableDS, Cluster.Major, Cluster.minor)
tableDS |
a |
Cluster.Major |
Number of the cluster where the major isoform belongs to |
Cluster.minor |
Number(s) of the cluster(s) where the minor isoform(s) belongs to (see details) |
When minor isoforms belong to different clusters, tableDS
codifies them using "&". For instance: clusters 1 and 2,
will be represented as "1&2". In such cases quotation marks must be used (see examples).
When minor isoforms are only in one cluster there is no need to use quotation marks.
A vector with the names of the genes.
Maria Jose Nueda, mj.nueda@ua.es
Nueda, M.J., Martorell, J., Marti, C., Tarazona, S and Conesa, A. 2017. Identification and visualization of differential isoform expression in RNA-Seq time series. In preparation.
Nueda, M.J., Tarazona, S., Conesa, A. 2014. Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series. Bioinformatics, 30, 2598-602.
Conesa, A., Nueda M.J., Alberto Ferrer, A., Talon, T. 2006. maSigPro: a Method to Identify Significant Differential Expression Profiles in Time-Course Microarray Experiments. Bioinformatics 22, 1096-1102.
data(ISOdata) data(ISOdesign) mdis <- make.design.matrix(ISOdesign) MyIso <- IsoModel(data=ISOdata[,-1], gen=ISOdata[,1], design=mdis, counts=TRUE) Myget <- getDS(MyIso) see <- seeDS(Myget, cluster.all=FALSE, k=6) table <- tableDS(see) table$IsoTable getDSPatterns(table, 1, 4) getDSPatterns(table, "1", "4") #will give the same result. getDSPatterns(table, 1, "1&5")