Source code using ||. Check if all of them are OK.
COUNT.TEST.R-65- g1 = which( lev[ 1 ] == group )
COUNT.TEST.R-66- g2 = which( lev[ 2 ] == group )
COUNT.TEST.R:67: idx = (rowSums( dc[ , g1 ] )/length(g1) >= minCountPerIndv ||
COUNT.TEST.R-68- rowSums( dc[ , g2 ] )/length(g2) >= minCountPerIndv )
COUNT.TEST.R-69- x = x[ idx ]
--
divergenceBuilder.R-44- Check <- ArgumentCheck::newArgCheck()
divergenceBuilder.R-45- cn = names(columns)
divergenceBuilder.R:46: if (!is.element('seqnames', cn) || !is.element('start', cn)) {
divergenceBuilder.R-47- ArgumentCheck::addError(
divergenceBuilder.R-48- msg = "You must provide the numbers for 'seqnames' (chromosomes names), 'start' columns",
--
KStest.R-38- if ( CDF == "GGamma 4P" ) { x = ((x - pars[ 3 ] )/pars[ 2 ] )^pars[ 1 ]; pars = pars[ 4 ] }
KStest.R-39-
KStest.R:40: if ( missing( sample.size ) || sample.size >= round( length( x ) ) )
KStest.R-41- sample.size = round( length( x )/3 )
KStest.R-42-
--
readCounts2GRangesList.R-50- }
readCounts2GRangesList.R-51- cn = names(columns)
readCounts2GRangesList.R:52: if (!is.element('seqnames', cn) || !is.element('start', cn)) {
readCounts2GRangesList.R-53- ArgumentCheck::addError(
readCounts2GRangesList.R-54- msg = "You must provide the numbers for 'seqnames' (chromosomes names), 'start' columns",
--
uniqueGRanges.R-72- m = rep(missing, l)
uniqueGRanges.R-73- seq = as.vector(S4Vectors::mcols(seq)[S4Vectors::queryHits(hits), 1])
uniqueGRanges.R:74: if (class(seq) == "factor" || class(seq) == "character")
uniqueGRanges.R-75- {
uniqueGRanges.R-76- m[S4Vectors::subjectHits(hits)] <- as.character(seq)
--
Weibull3Ps.R-164-
Weibull3Ps.R-165- if (!inherits( FIT1, "try-error" )) {
Weibull3Ps.R:166: if (sum(summary(FIT1)$parameters[1:2,4] > 0.05) == 2 || coef(FIT1)[2] < 1e-07 ) {
Weibull3Ps.R-167- PASS1 = FALSE
Weibull3Ps.R-168- } else PASS1 = TRUE
--
Weibull3Ps.R-170- if (!inherits( FIT2, "try-error" )) {
Weibull3Ps.R-171- suma = sum(summary(FIT2)$parameters[1:3,4] > 0.05)
Weibull3Ps.R:172: if (suma == 3 || coef(FIT2)[2] < 1e-07 || coef(FIT2)[3] < 0) {
Weibull3Ps.R-173- PASS2 = FALSE
Weibull3Ps.R-174- } else PASS2 = TRUE
--
Weibull3Ps.R-206-
Weibull3Ps.R-207- rm(FIT1,FIT2)
Weibull3Ps.R:208: if (PASS1 || PASS2)
Weibull3Ps.R-209- {
Weibull3Ps.R-210- # **** R squares ****
Weibull3Ps.R-211- Adj.R.Square = 1 - (deviance( FIT ) / ((n - length(coef(FIT))) * var(pX, use = "everything")))
Weibull3Ps.R:212: Adj.R.Square = ifelse(is.na(Adj.R.Square) || Adj.R.Square < 0, 0, Adj.R.Square)
Weibull3Ps.R-213-
Weibull3Ps.R-214- # Stain adjusted R square
Edited by JOSE RAUL BARRERAS MILANES