MS Protein Melting Data

Description Usage Arguments Details Value Examples

Model a single protein from an MSThermExperiment object.

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)

`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

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

MSThermResult object

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)