fix(utils): update all calls to getSeqLengths using getGenome

Author: jamespeapen

R/getABSignal.R

@@ -21,7 +21,7 @@
 #' #Modified from https://www.biostars.org/p/225520/
 #' random_genomic_int <- data.frame(chr = rep("chr14", 100))
 #' random_genomic_int$start <- apply(random_genomic_int, 1, function(x) {
-#'   round(runif(1, 0, getSeqLengths(chr = x)[[1]]), 0)
+#'   round(runif(1, 0, getSeqLengths(getGenome("hg19"), chr = x)[[1]]), 0)
 #' })
 
 #' random_genomic_int$end <- random_genomic_int$start + runif(1, 1, 1000)

R/getCorMatrix.R

@@ -20,7 +20,7 @@
 #' # Modified from https://www.biostars.org/p/225520/
 #' random_genomic_int <- data.frame(chr = rep("chr14", 100))
 #' random_genomic_int$start <- apply(random_genomic_int, 1, function(x) { 
-#'   round(runif(1, 0, getSeqLengths(chr = x)[[1]]), 0)
+#'   round(runif(1, 0, getSeqLengths(getGenome("hg19"), chr = x)[[1]]), 0)
 #' })
 #' random_genomic_int$end <- random_genomic_int$start + runif(1, 1, 1000)
 #' random_genomic_int$strand <- "*"

R/plotAB.R

@@ -33,7 +33,7 @@
 #' # Modified from https://www.biostars.org/p/225520/
 #' random_genomic_int <- data.frame(chr = rep("chr14", 100))
 #' random_genomic_int$start <- apply(random_genomic_int, 1, function(x) { 
-#'   round(runif(1, 0, getSeqLengths(chr = x)[[1]]), 0)
+#'   round(runif(1, 0, getSeqLengths(getGenome("hg19"), chr = x)[[1]]), 0)
 #' })
 #' random_genomic_int$end <- random_genomic_int$start + runif(1, 1, 1000)
 #' random_genomic_int$strand <- "*"