API for zhixingfeng/rGDA
What the package does (short line)

Global functions
ann_check_nccontig Source code
ann_contig_to_adjmat Source code
assemble Source code
assemble.core Source code
assemble.core.recode Source code
assemble.trim.centroid Source code
assemble.trim.centroid.core Source code
assemble_centroid Source code
assign.reads.to.centroids Source code
binom.bf Source code
bmf Source code
cal.dist Source code
cal.logLR Source code
cal.logLR.H0 Source code
cal.logLR.H1 Source code
cal.nlogn Source code
calCondFreq Source code
calLinkDist Source code
check.contain Source code
check.m5 Source code
check_contained_reads Source code
check_link_loci Source code
cluster.knn Source code
const.haplotype Source code
conv_encode_to_mat Source code
correct.reads Source code
countfreq Source code
cutwindow Source code
decode.snv Source code
detect.multiple Source code
detect.single Source code
detect.single.legacy Source code
dforest_link_loci_olc Source code
dist_hamming Source code
encode.snp Source code
eval.ann Source code
eval.ann.legacy Source code
eval.centroid Source code
eval.consensus Source code
filter_pileup_var Source code
findReadsByLoci Source code
find_read_pairs Source code
get.depth Source code
get.depth.samtools Source code
get.haplo.seq Source code
get.movie Source code
getReadsByID Source code
getVarComb Source code
get_cons_bymovie Source code
get_consensus Source code
get_consensus_recode Source code
get_nccontig Source code
getsnpmat Source code
kmeans_reads Source code
kmeans_reads_core Source code
link.scafold Source code
link.scafold.bak Source code
load.annfile Source code
load.cmpreadsfile Source code
load.dist Source code
load.encodefile Source code
load.jaccardfile Source code
load.m4file Source code
load.m5file Source code
load.output Source code
load.snp.code Source code
load.testfile Source code
load.varfile Source code
mat_fac Source code
mat_fac_long_reads_first Source code
mat_fac_mindist Source code
mat_fac_old Source code
mat_fac_rank_1 Source code
mat_fac_rank_1_core Source code
mat_fac_rm_redudant Source code
merge.scafold Source code
merge.scafold.core Source code
merge.scafold.extend Source code
merge.scafold.extend.core Source code
merge_centroid Source code
mix.m5 Source code
mod.cluster Source code
mod.cluster.core Source code
mod.cluster.sub Source code
olc Source code
parse.cigar Source code
parse.nucmer Source code
parse.snp Source code
pileup_reads Source code
pileup_reads_count Source code
pileup_var Source code
pileup_var_count Source code
pileup_var_count_recode Source code
plot.encode.data Source code
prefix_tree_cluster Source code
print_pileup Source code
read.context Source code
read.pileup Source code
read.similarity Source code
read.similarity.core Source code
reads.to.graph Source code
rm.isolated.nodes Source code
sample.reads Source code
save.encodefile Source code
save.m5file Source code
sclust Source code
sim_jaccard Source code
slide_win_clustering_core Source code
summary Source code
trim.m5 Source code
trim_centroid Source code
unconvolve.scafold Source code
validate.data Source code
zhixingfeng/rGDA documentation built on Oct. 13, 2018, 4:35 a.m.