SpotStats: spotStats

Description Usage Arguments Value

View source: R/internal_fluo_est.R

Description

It produces a table of estimated spot locations and fluorescence signals accompanied by informative plots. It can process the results of either spotCoords() for fluorescence-based estimation or forceBF() for BF image modelling estimation.

Usage

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SpotStats(img, chaImgs, binChaImgs, center, other.spots, BFcoords, BFarea,
  log.transform, warning, minDiff, separator, image.type)

Arguments

img

Data matrix. The original data of the BF image to be read and processed.

chaImgs

List. A list of the channel images (data matrices) of a sample.

binChaImgs

List. A list of binary segmented channel image data.

center

Data matrix. The 2-dimensional location of the spot's representative center.

BFcoords

List. A list of statistics describing the C1 chip line patterns (for BF image modelling).

BFarea

Integer. Defines a rectangular pseudo-spot size whose fluorescence will be estimated. This is mainly used in BF image modeling where a fluorescence spot could not be originally detected. The value of this parameter is also used as a cut-off to find matched spots across channel of the same sample image.

log.transform

Logical. If TRUE the image data are plotted in the log scale.

warning

Character string. An indicator of the estimation type that has been internally performed, i.e. fluorescence-based or BF image modelling.

minDiff

Float. the mu_hat of the H0: image-to-noise ratio = log(foreground_signal) - log(background_signal) = mu_hat. Rejection of H0 implies that the identified spot is brighter than background. Default is 0.5.

separator

Character string. Removes the Bright Field ("BF") and channel indicators from the image file names (see <<separator2>> in readFiles()).

image.type

Character string. A triplet of IDs to characterize the type of images under study. They refer to the ImageType part of the original image or txt file names.

Value

A table of location and fluorescence estimated with accompanied plots


CONFESS documentation built on Nov. 8, 2020, 6:05 p.m.