Index

_

__contains__() (pysnptools.util.IntRangeSet method) __delitem__() (pysnptools.util.IntRangeSet method) __eq__() (pysnptools.util.IntRangeSet method) __firstlineno__ (pysnptools.util.IntRangeSet attribute) __ge__() (pysnptools.util.IntRangeSet method) __getitem__() (pysnptools.util.IntRangeSet method) __gt__() (pysnptools.util.IntRangeSet method) __hash__ (pysnptools.util.IntRangeSet attribute) __iadd__() (pysnptools.util.IntRangeSet method) __iand__() (pysnptools.util.IntRangeSet method) __imul__() (pysnptools.util.IntRangeSet method) __init__() (pysnptools.util.IntRangeSet method) __ior__() (pysnptools.util.IntRangeSet method) __isub__() (pysnptools.util.IntRangeSet method)

__iter__() (pysnptools.util.IntRangeSet method) __ixor__() (pysnptools.util.IntRangeSet method) __le__() (pysnptools.util.IntRangeSet method) __len__() (pysnptools.util.IntRangeSet method) __lt__() (pysnptools.util.IntRangeSet method) __mul__() (pysnptools.util.IntRangeSet method) __ne__() (pysnptools.util.IntRangeSet method) __or__() (pysnptools.util.IntRangeSet method) __repr__() (pysnptools.util.IntRangeSet method) __reversed__() (pysnptools.util.IntRangeSet method) __static_attributes__ (pysnptools.util.IntRangeSet attribute) __str__() (pysnptools.util.IntRangeSet method) __sub__() (pysnptools.util.IntRangeSet method) __xor__() (pysnptools.util.IntRangeSet method)

A

add() (pysnptools.util.IntRangeSet method) allclose() (pysnptools.distreader.DistData method) (pysnptools.kernelreader.KernelData method) (pysnptools.pstreader.PstData method) (pysnptools.snpreader.SnpData method), [1]

array_module() (in module pysnptools.util) as_dist() (pysnptools.snpreader.SnpReader method), [1] as_snp() (pysnptools.distreader.DistReader method) asnumpy() (in module pysnptools.util)

B

Bed (class in pysnptools.snpreader), [1]

Beta (class in pysnptools.standardizer) Bgen (class in pysnptools.distreader)

C

clear() (pysnptools.util.IntRangeSet method) col (pysnptools.pstreader.PstReader property) (pysnptools.snpreader.Bed property) (pysnptools.snpreader.DistributedBed property) (pysnptools.snpreader.SnpGen property) (pysnptools.snpreader.SnpHdf5 property) (pysnptools.snpreader.SnpNpz property) col_count (pysnptools.pstreader.PstReader property) col_property (pysnptools.pstreader.PstReader property) (pysnptools.snpreader.Bed property) (pysnptools.snpreader.DistributedBed property) (pysnptools.snpreader.SnpGen property)

col_to_index() (pysnptools.pstreader.PstReader method) copy() (pysnptools.util.IntRangeSet method) copyinputs() (pysnptools.snpreader.Bed method) (pysnptools.snpreader.Dat method) (pysnptools.snpreader.DistributedBed method) (pysnptools.snpreader.Ped method) (pysnptools.snpreader.SnpGen method) (pysnptools.snpreader.SnpReader method) count() (pysnptools.util.IntRangeSet method) create_directory_if_necessary() (in module pysnptools.util)

D

Dat (class in pysnptools.snpreader), [1] default_id_rsid_function() (in module pysnptools.distreader.bgen) default_iid_function() (in module pysnptools.distreader.bgen) default_sample_function() (in module pysnptools.distreader.bgen) default_sid_function() (in module pysnptools.distreader.bgen) Dense (class in pysnptools.snpreader), [1] DiagKtoN (class in pysnptools.kernelstandardizer) (class in pysnptools.standardizer) DiagKtoNTrained (class in pysnptools.kernelstandardizer) (class in pysnptools.standardizer)

difference() (pysnptools.util.IntRangeSet method) difference_update() (pysnptools.util.IntRangeSet method) discard() (pysnptools.util.IntRangeSet method) DistData (class in pysnptools.distreader) DistGen (class in pysnptools.distreader) DistHdf5 (class in pysnptools.distreader) DistMemMap (class in pysnptools.distreader) DistNpz (class in pysnptools.distreader) DistReader (class in pysnptools.distreader) DistributedBed (class in pysnptools.snpreader), [1]

E

empty() (pysnptools.distreader.DistMemMap static method) (pysnptools.pstreader.PstMemMap static method) (pysnptools.snpreader.SnpMemMap static method), [1]

example_file() (in module pysnptools.util)

F

file_exists() (pysnptools.util.filecache.FileCache method) FileCache (class in pysnptools.util.filecache) filename (pysnptools.distreader.DistMemMap property) (pysnptools.pstreader.PstMemMap property) (pysnptools.snpreader.SnpMemMap property), [1]

flush() (pysnptools.distreader.Bgen method) (pysnptools.distreader.DistMemMap method) (pysnptools.pstreader.PstHdf5 method) (pysnptools.pstreader.PstMemMap method) (pysnptools.snpreader.SnpMemMap method), [1] format_delta() (in module pysnptools.util)

G

genwrite() (pysnptools.distreader.Bgen static method)

get_array_module() (in module pysnptools.util) getmtime() (pysnptools.util.filecache.FileCache method)

H

Hashdown (class in pysnptools.util.filecache)

Hdf5 (class in pysnptools.snpreader)

I

Identity (class in pysnptools.kernelreader) (class in pysnptools.kernelstandardizer) (class in pysnptools.standardizer) iid (pysnptools.distreader.DistReader property) (pysnptools.kernelreader.KernelReader property) (pysnptools.snpreader.SnpReader property), [1] iid0 (pysnptools.kernelreader.KernelReader property) iid0_count (pysnptools.kernelreader.KernelReader property) iid0_to_index() (pysnptools.kernelreader.KernelReader method) iid1 (pysnptools.kernelreader.KernelReader property) iid1_count (pysnptools.kernelreader.KernelReader property) iid1_to_index() (pysnptools.kernelreader.KernelReader method) iid_count (pysnptools.distreader.DistReader property) (pysnptools.kernelreader.KernelReader property) (pysnptools.snpreader.SnpReader property), [1]

iid_to_index() (pysnptools.distreader.DistReader method) (pysnptools.kernelreader.KernelReader method) (pysnptools.snpreader.SnpReader method), [1] index() (pysnptools.util.IntRangeSet method) intersect_apply() (in module pysnptools.util) intersect_ids() (in module pysnptools.util) intersection() (pysnptools.util.IntRangeSet method) intersection_update() (pysnptools.util.IntRangeSet method) IntRangeSet (class in pysnptools.util) ip_address() (in module pysnptools.util.filecache) ip_address_pid() (in module pysnptools.util.filecache) is_constant (pysnptools.standardizer.Standardizer property) isdisjoint() (pysnptools.util.IntRangeSet method) isempty (pysnptools.util.IntRangeSet property) issubset() (pysnptools.util.IntRangeSet method) issuperset() (pysnptools.util.IntRangeSet method)

J

join() (pysnptools.util.filecache.FileCache method)

K

kernel() (pysnptools.snpreader.SnpReader method), [1] KernelData (class in pysnptools.kernelreader) KernelHdf5 (class in pysnptools.kernelreader)

KernelNpz (class in pysnptools.kernelreader) KernelReader (class in pysnptools.kernelreader) KernelStandardizer (class in pysnptools.kernelstandardizer)

L

load() (pysnptools.util.filecache.FileCache method) load_hashdown() (pysnptools.util.filecache.Hashdown static method) loadOnePhen() (in module pysnptools.util.pheno) loadPhen() (in module pysnptools.util.pheno) Local (class in pysnptools.util.mapreduce1.runner)

LocalCache (class in pysnptools.util.filecache) LocalInParts (class in pysnptools.util.mapreduce1.runner) LocalMultiProc (class in pysnptools.util.mapreduce1.runner) LocalMultiThread (class in pysnptools.util.mapreduce1.runner) log_in_place() (in module pysnptools.util)

M

map_reduce() (in module pysnptools.util.mapreduce1), [1] max() (pysnptools.util.IntRangeSet method) min() (pysnptools.util.IntRangeSet method) module pysnptools pysnptools.distreader pysnptools.kernelreader pysnptools.pstreader pysnptools.snpreader pysnptools.standardizer pysnptools.util pysnptools.util.filecache pysnptools.util.mapreduce1 pysnptools.util.pheno

N

name (pysnptools.util.filecache.FileCache property) (pysnptools.util.filecache.Hashdown property) (pysnptools.util.filecache.LocalCache property) (pysnptools.util.filecache.PeerToPeer property)

O

offset (pysnptools.distreader.DistMemMap property) (pysnptools.pstreader.PstMemMap property) (pysnptools.snpreader.SnpMemMap property), [1]

open_read() (pysnptools.util.filecache.FileCache method) open_write() (pysnptools.util.filecache.FileCache method)

P

Ped (class in pysnptools.snpreader), [1] PeerToPeer (class in pysnptools.util.filecache) Pheno (class in pysnptools.snpreader), [1] pop() (pysnptools.util.IntRangeSet method) pos (pysnptools.distreader.DistReader property) (pysnptools.kernelreader.SnpKernel property) (pysnptools.snpreader.SnpReader property), [1] print2() (in module pysnptools.util) PstData (class in pysnptools.pstreader) PstHdf5 (class in pysnptools.pstreader) PstMemMap (class in pysnptools.pstreader) PstNpz (class in pysnptools.pstreader) PstReader (class in pysnptools.pstreader) pysnptools module pysnptools.distreader module

pysnptools.kernelreader module pysnptools.pstreader module pysnptools.snpreader module pysnptools.standardizer module pysnptools.util module pysnptools.util.filecache module pysnptools.util.mapreduce1 module pysnptools.util.pheno module

R

ranges() (pysnptools.util.IntRangeSet method) ranges_getitem() (pysnptools.util.IntRangeSet method) ranges_index() (pysnptools.util.IntRangeSet method) ranges_len (pysnptools.util.IntRangeSet property) read() (pysnptools.distreader.DistReader method) (pysnptools.kernelreader.KernelReader method) (pysnptools.pstreader.PstReader method) (pysnptools.snpreader.SnpReader method), [1] read_kernel() (pysnptools.snpreader.SnpReader method), [1] read_snps() (pysnptools.kernelreader.SnpKernel method) remove() (pysnptools.util.filecache.FileCache method) (pysnptools.util.IntRangeSet method)

rmtree() (pysnptools.util.filecache.FileCache method) row (pysnptools.pstreader.PstReader property) (pysnptools.snpreader.Bed property) (pysnptools.snpreader.DistributedBed property) (pysnptools.snpreader.SnpGen property) (pysnptools.snpreader.SnpHdf5 property) (pysnptools.snpreader.SnpNpz property) row_count (pysnptools.pstreader.PstReader property) row_property (pysnptools.distreader.DistReader property) (pysnptools.pstreader.PstReader property) (pysnptools.snpreader.SnpReader property), [1] row_to_index() (pysnptools.pstreader.PstReader method) Runner (class in pysnptools.util.mapreduce1.runner)

S

save() (pysnptools.util.filecache.FileCache method) save_hashdown() (pysnptools.util.filecache.Hashdown method) scan_local() (pysnptools.util.filecache.Hashdown static method) shape (pysnptools.pstreader.PstReader property) sid (pysnptools.distreader.DistReader property) (pysnptools.kernelreader.SnpKernel property) (pysnptools.snpreader.SnpReader property), [1] sid_count (pysnptools.distreader.DistReader property) (pysnptools.kernelreader.SnpKernel property) (pysnptools.snpreader.SnpReader property), [1] sid_to_index() (pysnptools.distreader.DistReader method) (pysnptools.snpreader.SnpReader method), [1] snp_gen() (in module pysnptools.util) SnpData (class in pysnptools.snpreader), [1]

SnpGen (class in pysnptools.snpreader), [1] SnpHdf5 (class in pysnptools.snpreader), [1] SnpKernel (class in pysnptools.kernelreader) SnpMemMap (class in pysnptools.snpreader), [1] SnpNpz (class in pysnptools.snpreader), [1] SnpReader (class in pysnptools.snpreader), [1] standardize() (pysnptools.kernelreader.KernelData method) (pysnptools.kernelstandardizer.KernelStandardizer method) (pysnptools.snpreader.SnpData method), [1] (pysnptools.standardizer.Standardizer method) Standardizer (class in pysnptools.standardizer) sub_matrix() (in module pysnptools.util) sum() (pysnptools.util.IntRangeSet method) symmetric_difference() (pysnptools.util.IntRangeSet method) symmetric_difference_update() (pysnptools.util.IntRangeSet method)

T

train_standardizer() (pysnptools.snpreader.SnpData method), [1]

U

union() (pysnptools.util.IntRangeSet method) Unit (class in pysnptools.standardizer)

UnitTrained (class in pysnptools.standardizer) update() (pysnptools.util.IntRangeSet method)

V

val (pysnptools.distreader.DistData property) (pysnptools.distreader.DistMemMap property) (pysnptools.kernelreader.KernelData property) (pysnptools.pstreader.PstData property) (pysnptools.pstreader.PstMemMap property) (pysnptools.snpreader.SnpData property), [1] (pysnptools.snpreader.SnpMemMap property), [1]

val_shape (pysnptools.distreader.DistReader property) (pysnptools.kernelreader.KernelReader property) (pysnptools.pstreader.PstData property) (pysnptools.snpreader.SnpReader property), [1]

W

walk() (pysnptools.util.filecache.FileCache method) weighted_mean() (in module pysnptools.util) weighted_simple_linear_regression() (in module pysnptools.util) write() (pysnptools.distreader.Bgen static method) (pysnptools.distreader.DistHdf5 static method) (pysnptools.distreader.DistMemMap static method) (pysnptools.distreader.DistNpz static method) (pysnptools.kernelreader.KernelHdf5 static method) (pysnptools.kernelreader.KernelNpz static method) (pysnptools.pstreader.PstHdf5 static method) (pysnptools.pstreader.PstMemMap static method) (pysnptools.pstreader.PstNpz static method) (pysnptools.snpreader.Bed static method), [1] (pysnptools.snpreader.Dat static method), [1] (pysnptools.snpreader.Dense static method), [1] (pysnptools.snpreader.DistributedBed static method), [1] (pysnptools.snpreader.Ped static method), [1] (pysnptools.snpreader.Pheno static method), [1] (pysnptools.snpreader.SnpHdf5 static method), [1] (pysnptools.snpreader.SnpMemMap static method), [1] (pysnptools.snpreader.SnpNpz static method), [1]