evaluate.Features: evaluate.Features

Description Usage Arguments Details Value Author(s)

Description

Evaluates feature consistency within analytical/technical replicates of samples based on PID or CV. Reports quantile distribution of PID or CV within technical replicates across all samples and computes a quantitative reproducibility score, QRscore, which is defined as the ratio of percentage of biological samples for which more than 50 percent of technical replicates have a signal and median PID or CV

Usage

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evaluate.Features(curdata, numreplicates, min.samp.percent = 0.6, alignment.tool, 
    impute.bool, missingvalue = 0)

Arguments

curdata

Feature table from apLCMS or XCMS with sample intensities.

numreplicates

Number of replicates per sample. eg: 2

min.samp.percent

If signal is detected in x proportion of technical replicates, then the missing values are replaced by mean intensity which is calculated using non-missing replicates. Defaul: 0.6

alignment.tool

Name of the feature alignment tool eg: "apLCMS" or "XCMS".

impute.bool

Logical (TRUE or FALSE). Used for calculating coefficient of variation (CV). Missing values are replaced by the mean of the non-missing intensities if at least 60 replicates have values. For example, if two out of three replicates have non-missing values (intensity >0) and the third replicate has a missing value (intensity=0), then the intensity of the third replicate is replaced by the mean of the intensities of the other two to calculate CV.

missingvalue

How are the missing values represented? eg: 0 or NA

Details

The function calculates Percent Intensity Difference (PID) or Percent Coefficient of Variation (CV) if there are two, or more than two replicates, respectively. PID is defined as percent ratio of the absolute difference of replicate intensities and the mean of replicate intensities. CV is defined as percent ratio of standard deviation of replicate intensities and mean of replicate intensities.

Value

Matrix with summary of feature consistency (min,first quartile (25th percentile), mean,median, third quartile (75th percentile), max,numgoodsamples, and QRscore). QRscore=Percent good samples/median PID or CV

Author(s)

Karan Uppal <kuppal2@emory.edu>


BowenNCSU/xMSanalyzer documentation built on May 24, 2019, 7:36 a.m.