get.mutland: Prepare data for 'plot.landscape'
In lixiangchun/lxctk: Li Xiangchun's tool-kit (lxctk)

Description Usage Arguments Details See Also Examples

Prepare mutational landscape data for plot.landscape. Automatically selected q-value cutoff to nominate SMGs.

1	get.mutland(genes=NULL, mutsigcv.sig.gene.file, gene.mut.freq.file, mut.per.smp.file, gene.mut.mat.file, use.q.value=TRUE, discard.genes=c("TTN"))

`genes`	A vector of gene symbols to be selected, if NULL automatically select SMGs.
`mutsigcv.sig.gene.file`	MutSigCV output file, often suffixed with `*.sig_genes.txt`.
`gene.mut.freq.file`	Gene mutation frequency file.
`mut.per.smp.file`	Mutation per sample file.
`gene.mut.mat.file`	Gene mutation matrix file.
`use.q.value`	Use q-value in `mutsigcv.sig.gene.file`, else use p-value.
`discard.genes`	Gene to be ignored in `genes`.

mutsigcv.sig.gene.file is generated by MutSigCV.

gene.mut.freq.file, mut.per.smp.file, gene.mut.mat.file can be generaed by ngstk1.0 muMat.

plot.landscape, plot.landscape2

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# Not run
r=get.mutland(genes=NULL, "../MutSigCV/GC.WES.sig_genes.txt", "../basic_stats/WES.exonic.gene_mut_freq.txt", "../basic_stats/WES.exonic.mut_per_sample.txt", "../basic_stats/WES.exonic.gene_mut_mat.txt", F, top.k.gene=13, discard.genes="TTN")