PTM: Pavlidis Template Matching

In axm323/dataVisEasy: datavisEasy: Data visualizations Using Annotations Made Easy

Pavlidis Template Matching

Description

a simple implementation of Pavlidis Template Matching that searches for correlations above a specified threshold within the supplied input data. Templates can be annotations, genes or samples, or a cusotm template can be provided.

Usage

PTM(data, match.template, annotation.level.set.high, custom.template = NA,
  Find.Match.For = "genes",cutoff = 0.05, cut.by = "pvals", method = "pearson",
  NA.handling = "pairwise.complete.obs", return.vals = FALSE)

Arguments

data	numeric data matrix with samples/observations in the columns and genes/variables in the rows
match.template	template to be matched against. If Find.Match.For = "genes", can supply a gene to be matched against (rownames in input data) or a string pointing to an annotation stored in the annotations dataframe in the params list object. If Find.Match.For = "samples", can supply a sample to be matched against (colnames in input data) or a string pointing to an annotation stored in the annotations.genes dataframe in the params list object.
annotation.level.set.high	a character vector indicating which levels of an annotation factor to set high. match.template will point to an annotation stored in the params list object, levels supplied here will be set to 1 while all other levels will be set to 0, searching for matches that have high expression for the given levels and low expression for all others
custom.template	a custom template to be matched against. Must be the same length as columns of input data if Find.Match.For = "genes" or the same length as rows of input data if Find.Match.For = "samples"
Find.Match.For	whether matches should be found for genes or samples, accepts "genes" (default) or "samples"
cutoff	the cutoff for which matches are determined to be significant. should be set according to cut.by. Default of 0.05 assumes cut.by = "pvals".
cut.by	whether to use the pvalues ("pvals", default) or correlations ("rvals") as the cutoff for significant matches. If "pvals", will return matches that have a pvalue below "cutoff" and with a correlation > 0 (only positive correlations not negative correlation). If "rvals", will return matches that have correlation > cutoff.
method	method to be used to correlation. Accepts values to be passed to cor() such as "pearson" (default), "spearman", and "kendall".
NA.handling	how missing values should be handled in the case of correlations, passed to the "use" argument of cor()
return.vals	logical of whether or not to return pvalues and correlation values for all comparisons. If FALSE (default), will return a list of genes or samples that passed the threshold set by cutoff. If TRUE, will return a dataframe containing the pvalues and correlations for each item with respect to the template.

Details

Will compute all correlations for the rows/columns of the input data compared to a provided template using the indicated correlation method. Custom templates the same length as the rows/columns of the data can be provided or matched can be found to a specific gene (see corrs2Gene) or samples. Additionally, templates can be created based off of sample or gene annotations stored in the params list object.If pointing to an annotation stored in the params list object, levels supplied to "set.high" will be set to 1 while all other levels will be set to 0, searching for matches that have high expression for the given levels and low expression for all others.

Value

if return.vals == FALSE, will return a character vector of genes or samples that passed the pvalue or correlation cutoff indicated.

if return.vals == TRUE, will return a dataframe giving the pvalue and correlation value for each variable compared to the supplied template

Author(s)

~~Alison Moss~~

References

Pavlidis and Noble 2001

See Also

See params,set_annotations, set_annotations.genes, for more information on setting up annotations.

Examples

##initiate parameters and annotations
initiate_params()
set_annotations(RAGP_annots)

##using the "State" annotation, find genes were State A has high expression, return passes
A.high <- PTM(RAGP_norm, match.template = "State", annotation.level.set.high = "A")
head(A.high)
A.high.01 <- PTM(RAGP_norm, match.template = "State", annotation.level.set.high = "A",
  cutoff = 0.01)
head(A.high.01)

##return dataframe with pvalues and correlations to template
A.high.results <- PTM(RAGP_norm, match.template = "State", annotation.level.set.high = "A",
  , return.vals = TRUE)
head(A.high.results)


##find matches to a gene of interest
Th.match <- PTM(RAGP_norm, match.template = "Th", cut.by = "rvals", cutoff = 0.8)
Th.match

##the same can be applied to find matches for samples
##can also supply a custom vector to be matched against

axm323/dataVisEasy documentation built on Feb. 1, 2024, 11:53 p.m.