R/utils_ImportSesameData.R
ImportSesameData.RdLoad either the HM540 and EPIC manifests into working memory
ImportSesameData(manifest_char)Which manifest should be loaded? Currently, this package has been tested to work with 450k and EPIC arrays for HG19 and HG38.
This function assumes that the .onLoad() function has executed properly and (therefore) that the necessary data sets are in the cache.
hm450k_gr <- ImportSesameData("HM450.hg19.manifest")
#> snapshotDate(): 2021-05-18
#> see ?sesameData and browseVignettes('sesameData') for documentation
head(hm450k_gr)
#> GRanges object with 6 ranges and 52 metadata columns:
#> seqnames ranges strand | address_A address_B channel
#> <Rle> <IRanges> <Rle> | <integer> <integer> <character>
#> cg13869341 chr1 15865-15866 - | 62703328 16661461 Red
#> cg14008030 chr1 18827-18828 - | 27651330 <NA> Both
#> cg12045430 chr1 29407-29408 - | 25703424 34666387 Red
#> cg20826792 chr1 29425-29426 - | 61731400 14693326 Red
#> cg00381604 chr1 29435-29436 - | 26752380 50693408 Red
#> cg20253340 chr1 68849-68850 - | 49752305 <NA> Both
#> designType nextBase nextBaseRef probeType orientation
#> <character> <character> <character> <character> <character>
#> cg13869341 I A C cg down
#> cg14008030 II G/A C cg down
#> cg12045430 I A C cg down
#> cg20826792 I T A cg down
#> cg00381604 I A T cg down
#> cg20253340 II G/A C cg down
#> probeCpGcnt context35 probeBeg probeEnd ProbeSeq_A
#> <integer> <integer> <integer> <numeric> <character>
#> cg13869341 2 4 15865 15914 CCAATAACTAACCACTCTAC..
#> cg14008030 2 3 18828 18877 ACTCRAAATTTACTCAATAA..
#> cg12045430 8 11 29407 29456 AAAAAAAACACAATAAAAAA..
#> cg20826792 7 12 29425 29474 AATCCTAAAACCACACTCAA..
#> cg00381604 7 12 29435 29484 AAATCAACAAAATCCTAAAA..
#> cg20253340 1 1 68850 68899 ATTCTATCTCRCACTACTTC..
#> ProbeSeq_B gene
#> <character> <character>
#> cg13869341 CCGATAACTAACCACTCTAC.. WASH7P
#> cg14008030 MIR6859-3;WASH7P
#> cg12045430 GAAAAAAACGCAATAAAAAA.. MIR1302-9;RP11-34P13..
#> cg20826792 AATCCTAAAACCGCGCTCGA.. MIR1302-9;RP11-34P13..
#> cg00381604 GAATCGACGAAATCCTAAAA.. MIR1302-9;RP11-34P13..
#> cg20253340 OR4F5
#> gene_HGNC chrm_A beg_A flag_A mapQ_A
#> <character> <character> <integer> <integer> <integer>
#> cg13869341 WASH7P chr1 15865 16 17
#> cg14008030 MIR6859-3;WASH7P chr1 18828 16 1
#> cg12045430 MIR1302-9;RP11-34P13.. chr1 29407 16 4
#> cg20826792 MIR1302-9;RP11-34P13.. chr1 29425 16 4
#> cg00381604 MIR1302-9;RP11-34P13.. chr1 29435 16 4
#> cg20253340 OR4F5 chr1 68850 16 6
#> cigar_A NM_A chrm_B beg_B flag_B mapQ_B
#> <character> <integer> <character> <integer> <integer> <integer>
#> cg13869341 50M 0 chr1 15865 16 17
#> cg14008030 50M 0 <NA> <NA> <NA> <NA>
#> cg12045430 50M 0 chr1 29407 16 4
#> cg20826792 50M 0 chr1 29425 16 4
#> cg00381604 50M 0 chr1 29435 16 4
#> cg20253340 50M 0 <NA> <NA> <NA> <NA>
#> cigar_B NM_B wDecoy_chrm_A wDecoy_beg_A wDecoy_flag_A
#> <character> <integer> <character> <integer> <integer>
#> cg13869341 50M 0 chr1 15865 16
#> cg14008030 <NA> <NA> chr1 18828 16
#> cg12045430 50M 0 chr1 29407 16
#> cg20826792 50M 0 chr1 29425 16
#> cg00381604 50M 0 chr1 29435 16
#> cg20253340 <NA> <NA> chr1 68850 16
#> wDecoy_mapQ_A wDecoy_cigar_A wDecoy_NM_A wDecoy_chrm_B
#> <integer> <character> <integer> <character>
#> cg13869341 17 50M 0 chr1
#> cg14008030 1 50M 0 <NA>
#> cg12045430 4 50M 0 chr1
#> cg20826792 4 50M 0 chr1
#> cg00381604 4 50M 0 chr1
#> cg20253340 6 50M 0 <NA>
#> wDecoy_beg_B wDecoy_flag_B wDecoy_mapQ_B wDecoy_cigar_B
#> <integer> <integer> <integer> <character>
#> cg13869341 15865 16 17 50M
#> cg14008030 <NA> <NA> <NA> <NA>
#> cg12045430 29407 16 4 50M
#> cg20826792 29425 16 4 50M
#> cg00381604 29435 16 4 50M
#> cg20253340 <NA> <NA> <NA> <NA>
#> wDecoy_NM_B posMatch MASK_mapping MASK_typeINextBaseSwitch
#> <integer> <logical> <logical> <logical>
#> cg13869341 0 TRUE TRUE FALSE
#> cg14008030 <NA> TRUE TRUE FALSE
#> cg12045430 0 TRUE TRUE FALSE
#> cg20826792 0 TRUE TRUE FALSE
#> cg00381604 0 TRUE TRUE FALSE
#> cg20253340 <NA> TRUE TRUE FALSE
#> MASK_rmsk15 MASK_sub40_copy MASK_sub35_copy MASK_sub30_copy
#> <logical> <logical> <logical> <logical>
#> cg13869341 FALSE TRUE TRUE TRUE
#> cg14008030 FALSE FALSE FALSE FALSE
#> cg12045430 FALSE FALSE TRUE TRUE
#> cg20826792 FALSE FALSE FALSE FALSE
#> cg00381604 FALSE FALSE FALSE FALSE
#> cg20253340 FALSE TRUE TRUE TRUE
#> MASK_sub25_copy MASK_snp5_common MASK_snp5_GMAF1p MASK_extBase
#> <logical> <logical> <logical> <logical>
#> cg13869341 TRUE FALSE FALSE FALSE
#> cg14008030 FALSE FALSE FALSE FALSE
#> cg12045430 TRUE FALSE FALSE FALSE
#> cg20826792 FALSE FALSE FALSE FALSE
#> cg00381604 TRUE FALSE FALSE FALSE
#> cg20253340 TRUE FALSE FALSE FALSE
#> MASK_general
#> <logical>
#> cg13869341 TRUE
#> cg14008030 TRUE
#> cg12045430 TRUE
#> cg20826792 TRUE
#> cg00381604 TRUE
#> cg20253340 TRUE
#> -------
#> seqinfo: 26 sequences from an unspecified genome; no seqlengths