read.ShesisPlus.output: Read the haplotyping results from the ShesisPlus output

In PolyHaplotyper: Assignment of Haplotypes Based on SNP Dosages in Diploids and Polyploids

Description

Read the haplotyping results from the ShesisPlus output

Usage

read.ShesisPlus.output(SSPout, order.by=c("", "hapnr", "count")[2])

Arguments

SSPout	filename of a text file with ShesisPlus output (as copied from the web page produced by running ShesisPlus web interface at http://shesisplus.bio-x.cn/SHEsis.html); or a character vector with the same output
order.by	how to order the rows of the hapstat data.frame. "hapnr" means ordering by haplotype number, "count" means ordering by decreasing Total.count, anything else results in no reordering. By default order by hapnr.

Details

If present, the markernames and the haplotype statistics are read from the file. ShesisPlus does not provide haplotype combinations for individuals

Value

a list with 2 items: $markernames has the marker names in the markers in the haploblock (if present in the file); hapstat contains the haplotype statistics as read from the file with an additional (first) column hapnr: the haplotype numbers as defined in PolyHaplotyper. The other columns are Haplotype (as sequences of marker alleles), Total.count (of the haplotype over the whole population) and, according to an email from Zhiqiang Li of 13-04-2020) BETA: Regression coefficient, SE: Standard error, R2: Regression r-squared, T: t-distribution statistics, P: p-value

Examples

# we give a typical SSP output as character vector; instead we could also
# give the name of a text file
SSPout <- c(
 " Please cite:",
 "",
 "    Shen, J. et al. SHEsisPlus, a toolset for genetic studies ...",
 "    Shi, Y. et al. SHEsis, a powerful software platform ...",
 "    Li, Z. et al. A partition-ligation-combination-subdivision ...",
 "",
 "if you find this tool useful in your research. Thanks!",
 "",
 "Haplotype Analysis:",
 "",
 "Haplotypes with frequency <0.03 are ignored.",
 "Loci chosen for haplotype analysis: m1, m2, m3, m4",
 "Haplotype 	Total count 	Beta 	SE 	R2 	T 	p",
 "1122 	2232 	0.002 	0.01 	1.01e-04 	0.252 	0.8",
 "1222 	230 	-0.019 	0.017 	0.002 	-1.15 	0.25",
 "1221 	152 	-0.01 	0.024 	2.94e-04 	-0.43 	0.667",
 "2222 	288 	0.008 	0.02 	2.93e-04 	0.429 	0.667",
 "1121 	142 	-0.009 	0.022 	2.81e-04 	-0.42 	0.674"
)
read.ShesisPlus.output(SSPout)

PolyHaplotyper documentation built on June 17, 2021, 5:12 p.m.