plotValidationGenes: Plot Validation Genes
In ccchang0111/PAM50: Breast Cancer's PAM50 prediction based on patient's RNA-seq data

This plots distribution of validation genes (4 by default) for validating the prediction result.

1 2	plotValidationGenes(es, PAM50.pred, genes = c("ESR1", "PGR", "MKI67", "ERBB2"))

`es`	dataframe, rows are genes columns are samples. Row names has to be EntrezID.
`PAM50.pred`	array of each sample's PAM50 label
`genes`	(optional) vector of validation gene names

Default 4 genes:

"ERBB2": Her2 gene; Her2 group should have the highest ERBB2 value.

"ESR1": ER gene; LumA and LumB groups should have the highest ESR1 value.

"MKI67": tumor growth factor; LumA should have the lowest MKI67 value because LumA patients usually have the best prognosis.

"PGR": PR gene; LumA should have the highest PGR value.

ccchang0111/PAM50 documentation built on May 31, 2019, 5:40 a.m.

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