model_protein {mstherm}

Model single protein.

Description

Model a single protein from an MSThermExperiment object.

Usage

model_protein(expt, protein, min_rep_psm = 0, min_smp_psm = 0,
  min_tot_psm = 0, max_inf = 1, min_score, max_score, smooth = 0,
  method = "sum", method.denom = "near", trim = 0, bootstrap = 0,
  min_bs_psms = 8, annot_sep = "|", max_slope = 0, min_r2 = 0,
  min_reps = 0, only_modeled = 0, check_missing = 0,
  missing_cutoff = 0.3)

Arguments

expt

An MSThermExperiment object

protein

ID of the protein to model

min_rep_psm

Minimum number of spectral matches required for each replicate to model protein

min_smp_psm

Minimum number of spectral matches required for each sample to model protein

min_tot_psm

Minimum number of spectral matches required across all replicates to model protein

max_inf

Maximum co-isolation interference level allowed to include a spectrum in protein-level quantification

min_score

minimum score allowed to include a spectrum in protein-level quantification

max_score

maximum score allowed to include a spectrum in protein-level quantification

smooth

(t/F) Perform loess smoothing on the data prior to modeling

method

Protein quantification method to use (see Details)

method.denom

Method used to calculate denominator of abundance (see Details)

trim

(t/F) Trim all lower data points less than the abundance maximum

bootstrap

(T/F) Perform bootstrap analysis to determine confidence intervals (slow)

min_bs_psms

Minimum number of spectral matches required to perform bootstrapping

annot_sep

Symbol used to separate protein group IDs (used for retrieval of annotations) (default: '|')

max_slope

Maximum slope to consider model (implies "only_modeled")

min_r2

Minimum R2 value to consider model (implies "only_modeled")

min_reps

Minimum number of modeled replicates for each sample to return protein

only_modeled

(t/F) Only consider modeled proteins

check_missing

(t/F) Run simple test to filter out PSMs with missing quantification channels where values are expected

missing_cutoff

Minimum fraction relative to surrounding data points used in the check for missing channels

Details

Valid quantification methods include:

"sum"

use the sum of the spectrum values for each channel

"median"

use the median of the spectrum values for each channel

"ratio.median"

Like "median", but values for each spectrum are first converted to ratios according to "method.denom" channel

"ratio.mean"

Like "ratio.median" but using mean of ratios

Valid denominator methods include:

"first"

Use the first value (lowest temperature point) (default)

"max"

Use the maximum value

"top3"

Use the mean of the three highest values

"near"

Use the median of all values greater than 80 the first value

Value

MSThermResult object

Examples

control <- system.file("extdata", "demo_project/control.tsv", package="mstherm")
annots  <- system.file("extdata", "demo_project/annots.tsv",  package="mstherm")
expt    <- MSThermExperiment(control, annotations=annots)
expt    <- normalize_to_std(expt, "cRAP_ALBU_BOVIN", plot=FALSE)

model   <- model_protein(expt, "P38707", smooth=TRUE, bootstrap=FALSE)
summary(model)