bicrnaseq: MSKCC Bioinformatics Core RNASeq

Description Usage Arguments

Given the results of DESeq comparison of two conditions and the full normalized count matrix, generate a heatmap showing the relative expression values of "top 100" differentially expressed genes. If there are fewer than 100 genes in the results file, all of them will be included in the heatmap. Color scheme is red/black/green.

bic.standard.heatmap(norm.counts.matrix, condA, condB, genes = NULL,
  file = NULL)

bic.standard.heatmap(norm.counts.matrix, condA, condB, genes = NULL,
  file = NULL)

`norm.counts.matrix`	matrix of normalized counts, where a row is a gene and a column is a sample. May contain "GeneID" and/or "GeneSymbol" column. If GeneSymbol column is present, it will be used for heatmap labeling. If not, GeneID column will be used.
`condA`	the first condition named in the bic.deseq.file name
`condB`	the second condition named in the bic.deseq.file name
`genes`	a vector of genes to be included in the heatmap; if normalized counts matrix includes "GeneSymbol" column, genes must be from that column. Otherwise, they must be from the "GeneID" column.
`file`	name of PDF file to which heatmap should be written. (optional)
`norm.counts.matrix`	matrix of normalized counts, where a row is a gene and a column is a sample. May contain "GeneID" and/or "GeneSymbol" column. If GeneSymbol column is present, it will be used for heatmap labeling. If not, GeneID column will be used.
`condA`	the first condition named in the bic.deseq.file name
`condB`	the second condition named in the bic.deseq.file name
`genes`	a vector of genes to be included in the heatmap; if normalized counts matrix includes "GeneSymbol" column, genes must be from that column. Otherwise, they must be from the "GeneID" column.
`file`	name of PDF file to which heatmap should be written. (optional)