<html><body><div style="color:#000; background-color:#fff; font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:12pt"><div><span>Muitíssimo obrigada !!! </span></div><div class="yahoo_quoted" style="display: block;"> <br> <br> <div style="font-family: HelveticaNeue, 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif; font-size: 12pt;"> <div style="font-family: HelveticaNeue, 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif; font-size: 12pt;"> <div dir="ltr"> <font size="2" face="Arial"> Em Quinta-feira, 21 de Novembro de 2013 13:24, Éder Comunello <comunello.eder@gmail.com> escreveu:<br> </font> </div> <div class="y_msg_container"><div id="yiv9412316942"><div><div dir="ltr"><div>Giselle,</div><div><br clear="none"></div><div>Faltou usar a primeira coluna como row.names....</div><div><br clear="none"></div><div>Já atualizei o código que segue abaixo:</div><div><br
clear="none"></div><div><div><font face="courier new, monospace">### <BEGIN></font></div>
<div><font face="courier new, monospace">###</font></div><div><font face="courier new, monospace">browseURL('<a rel="nofollow" shape="rect" target="_blank" href="http://cran.r-project.org/web/packages/rrBLUP/vignettes/GS_tutorial.pdf">http://cran.r-project.org/web/packages/rrBLUP/vignettes/GS_tutorial.pdf</a>')</font></div>
<div><font face="courier new, monospace">###</font></div><div><font face="courier new, monospace">setwd("C:/LAB/Tmp"); getwd()</font></div><div><font face="courier new, monospace">dURL <- "<a rel="nofollow" shape="rect" target="_blank" href="https://www.crops.org/publications/tpg/supplements/5/tpg12-06-0006-dataset-s2.gz">https://www.crops.org/publications/tpg/supplements/5/tpg12-06-0006-dataset-s2.gz</a>"</font></div>
<div><font face="courier new, monospace">gzFile <- strsplit(dURL, "/")[[1]][8]; gzFile</font></div><div><font face="courier new, monospace"><br clear="none"></font></div><div><font face="courier new, monospace">### fazendo o download</font></div>
<div><font face="courier new, monospace">download.file(dURL, gzFile, mode='wb') </font></div><div><font face="courier new, monospace">### downloaded 4.3 Mb</font></div><div><font face="courier new, monospace"><br clear="none">
</font></div><div><font face="courier new, monospace">### uma vez baixados, os arquivos comprimidos com bzip2, xvz, ou gzip podem </font></div><div><font face="courier new, monospace">### ser lidos diretamente com read.table()</font></div>
<div><font face="courier new, monospace">GBS <- read.table(gzFile, sep=',', header=T, stringsAsFactors=F, row.names=1)</font></div><div><font face="courier new, monospace">dim(GBS)</font></div><div><font face="courier new, monospace">### [1] 41371 257</font></div>
<div><font face="courier new, monospace"><br clear="none"></font></div><div><font face="courier new, monospace">parse.GBS <- function(x) {</font></div><div><font face="courier new, monospace"> unique.x <- unique(x)</font></div>
<div><font face="courier new, monospace"> alleles <- setdiff(unique.x,union("H","N"))</font></div><div><font face="courier new, monospace"> y <- rep(0,length(x))</font></div><div><font face="courier new, monospace"> y[which(x==alleles[1])] <- -1</font></div>
<div><font face="courier new, monospace"> y[which(x==alleles[2])] <- 1</font></div><div><font face="courier new, monospace"> y[which(x=="N")] <- NA</font></div><div><font face="courier new, monospace"> return(y)</font></div>
<div><font face="courier new, monospace">}</font></div><div><font face="courier new, monospace"><br clear="none"></font></div><div><font face="courier new, monospace">X <- apply(GBS[,-c(1:3)],1,parse.GBS)</font></div><div><font face="courier new, monospace">dim(X)</font></div>
<div><font face="courier new, monospace">### [1] 254 41371</font></div><div><font face="courier new, monospace"><br clear="none"></font></div><div><font face="courier new, monospace">frac.missing <- apply(X,2,function(z){length(which(<a rel="nofollow" shape="rect" target="_blank" href="http://is.na/">is.na</a>(z)))/length(z)})</font></div>
<div><font face="courier new, monospace">length(which(frac.missing<0.5))</font></div><div><font face="courier new, monospace">### [1] 16030</font></div><div class="yiv9412316942yqt8567382720" id="yiv9412316942yqtfd04565"><div><font face="courier new, monospace"><br clear="none"></font></div><div><font face="courier new, monospace">hist(frac.missing)</font></div>
<div><font face="courier new, monospace">### OK!!!</font></div><div><font face="courier new, monospace"><br clear="none"></font></div><div><font face="courier new, monospace">### <END></font></div></div></div><div class="yiv9412316942yqt8567382720" id="yiv9412316942yqtfd39431"><br clear="none"><div class="yiv9412316942gmail_extra">
<br clear="all"><div><div dir="ltr">Éder Comunello <<a rel="nofollow" shape="rect" ymailto="mailto:comunello.eder@gmail.com" target="_blank" href="mailto:comunello.eder@gmail.com">c</a><a rel="nofollow" shape="rect" ymailto="mailto:omunello.eder@gmail.com" target="_blank" href="mailto:omunello.eder@gmail.com">omunello.eder@gmail.com</a>> <br clear="none">Dourados, MS - [22 16.5'S, 54 49'W]<br clear="none">
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