qualityRank {sesame}R Documentation

This function looks at public data of similar nature e.g., tissue, FFPE vs non-FFPE, etc to evaluate the quality of the target data quality

Description

This function looks at public data of similar nature e.g., tissue, FFPE vs non-FFPE, etc to evaluate the quality of the target data quality

Usage

qualityRank(sset, tissue = NULL, samplePrep = NULL, raw = FALSE)

Arguments

sset

a raw (unprocessed) SigSet

tissue

A string (blood,buccal and saliva)

samplePrep

FFPE, fresh, frozen

raw

to return the raw comparison table

Value

three numbers: 1. The number of public samples compared. 2. The fraction of public samples with more nondetection, and 3. The fraction of public samples with lower mean intensity 4. The higher the fraction, the better the sample.

Examples


sesameDataCache("EPIC") # if not done yet
sset <- sesameDataGet('EPIC.1.LNCaP')$sset
ranks <- qualityRank(sset)


[Package sesame version 1.8.10 Index]