PuInc_seeker: Detect Putative Incorporation features

Description Usage Arguments Value Examples

View source: R/PuInc_seeker.R

Description

Use Welch's T-test to detect features upregulated in labelled samples

Usage

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PuInc_seeker(XCMSet = NULL, XCMSmode = "maxo", ULtag = NULL,
  Ltag = NULL, separator = "_", sep.pos.front = TRUE,
  fc.threshold = 1.2, p.value.threshold = 0.05, PuInc.int.lim = NULL)

Arguments

XCMSet

xcmsSet object of samples processed by xcms workflow

XCMSmode

Type of quantification value for the features, as in xcms::groupval(XCMSet)

ULtag

Unlabelled sample name tag, for example "C12"

Ltag

Labelled sample name tag, for example "C13"

separator

Character used as separator in sample names, as in xcms::sampclass(XCMSet)

sep.pos.front

TRUE if position of ULtag and Ltag is found previous to the condition names. Check xcms::sampclass(XCMSet)

fc.threshold

Fold-change threshold for detection of upregulated features associated to Putative incorporation

p.value.threshold

p-Value threshhold between for detection of upregulated features associated to Putative incorporation

PuInc.int.lim

Intensity limit in unlabelled sample for the selection of features to be tested as possible Putative incorporation

Value

A list containing:

PuInc

Putative Incorporation Features matrix

PuInc_conditions

Experimetal conditions (as in xcms::sampclass(XCMSet)) in which PuInc were detected

pvalue

Matrix of p-values from the tested features

foldchange

Matrix of fold-changes from the tested features

params

Inputed arguments to be inherited by basepeak_finder

Examples

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data(mtbls213)
xcms::sampclass(mtbls213)
PuInc_seeker(XCMSet=mtbls213,ULtag="CELL_Glc12",Ltag="CELL_Glc13",
sep.pos.front=TRUE ,fc.threshold=1.5,p.value.threshold=.05,	PuInc.int.lim = 4000)

jcapelladesto/geoRge documentation built on Aug. 4, 2017, 12:14 a.m.