pce: Read gene data from PCE file

In BioSSA/BioSSA: A collection of methods for singular spectrum analysis of drosophila embryo (2d and 3d) gene expression

Description

Read gene expression data from PointCloud file

Usage

read.vpc(file)
read.pce(file)
extract.gene.vpc(vpc, gene, cohort)
extract.gene.pce(pce, gene, measurement = c("default", "apical", "basal", "nuclear", "cellular"))
read.vpc.gene(file, gene, ...)
read.pce.gene(file, gene, ...)

Arguments

file	character, PCE file name
gene	character, gene name for extraction
vpc	parsed VPC file content returned by read.vpc
pce	parsed PCE file content returned by read.pce
cohort	cohort number in VPC file
measurement	measurement kind
...	further arguments passed to extract.gene.vpc or extract.gene.pce (i.e., cohort or measurement)

Details

read.pce.gene is combination of read.pce and extract.gene.pce. read.vpc.gene is combination of read.vpc and extract.gene.vpc.

Value

Object of class ‘embryo3d’ for extract.gene.vpc, extract.gene.pce, read.vpc.gene, and read.pce.gene. Data frame with additional attributes for read.vpc and read.pce.

References

PCE format description: http://bdtnp.lbl.gov/Fly-Net/bioimaging.jsp?w=pceFormat VPC format description: http://bdtnp.lbl.gov/Fly-Net/bioimaging.jsp?w=vpcFormat

See Also

embryo3d, plot.embryo3d

Examples

file <- system.file("extdata/pce", "v5_s12166-23au07-22.pce", package = "BioSSA")
eve <- read.pce.gene(file, gene = "eve")
plot(eve, type = "hull")
plot(eve, type = "nuclei")


file <- system.file("extdata/vpc", "D_pse_wt_atlas_rc4.vpc", package = "BioSSA")
vpc <- read.vpc(file)
eve <- extract.gene.vpc(vpc, gene = "eve", cohort = 4)
plot(eve, type = "hull")
plot(eve, type = "nuclei")

BioSSA/BioSSA documentation built on May 5, 2019, 3:47 p.m.