lme_pqi: Calculate PQI using linear mixed effect model from q2e...

In ismaRP/MALDIpqi: Estimate Parchment Glutamine Index from MALDI-TOF datasets

Calculate PQI using linear mixed effect model from q2e estimates

Description

Calculate PQI using linear mixed effect model from q2e estimates

Usage

lme_pqi(q2e_vals, logq = TRUE, g = NULL, outdir = NULL, return_model = F)

Arguments

logq	Whether q values are log-scaled before entering the LME model
g	Reliability power in the error normal distribution from linear mixed effects model
outdir	Optional. directory where results tables and plots are saved
q2e	data.frame with q2e estimations per sample, replicate and peptide

Value

list contaning the following:

• sample: data.frame with aggregated PQI estimates per sample

• pep: data.frame of fitted and residuals per replicate and peptide

• estimates: list of model estimates

sample data.frame has the following columns:

• Sample: sample name

• Prediction: sample random effects obtained from custom formula that. It is the log(PQI)

• sd: log(PQI) standard error

• RanefModel: sample random effects, as calculated by ranef. It should be the same as Prediction, up to numerical precision

• PQI.Model, exponentials estimates. It is the PQI

pep data.frame contains:

• Sample, replicate and peptide IDs

• q: is the q calculated by the WLS from the isotopic distributions

• Reliability: minimum least square of q caluclated in the WLS step

• Loqq: log(q)

• resp: either q or log(q), according to whether logq was FALSE or TRUE

• Fitted: fitted q value

• Res: pearson residuals from Fitted

• Fitted0: fitted q values at the peptide level. It's equal to the peptide fixed effect

• Res0: pearson residuals from Fitted0

estimates list contains

• alpha: peptide fixed effects

• sigma2_S: sample random effect variance

• sigma2_R: replicate random effect variance

• gamma: Reliability 2·gamma exponent

• sigma2: peptide fixed effects variance

ismaRP/MALDIpqi documentation built on Dec. 28, 2024, 1:08 p.m.