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simulateBam

Source: R/simulateBam.R
simulateBam.Rd

This function creates sample BAM files given mandatory and optional BAM fields.

Usage

simulateBam(
  output.bam.file = NULL,
  qname = NULL,
  flag = NULL,
  rname = NULL,
  pos = NULL,
  mapq = NULL,
  cigar = NULL,
  rnext = NULL,
  pnext = NULL,
  tlen = NULL,
  seq = NULL,
  qual = NULL,
  ...,
  verbose = TRUE
)

Arguments

output.bam.file

output BAM file location string. If NULL (default), records are not written to BAM but returned as a data.table object for review.

qname

character vector of query names. When default (NULL), names like "q0001".."qNNNN" will be assigned.

flag

integer vector of bitwise flags (a combination of the BAM_F* constants). When default (NULL), zero (i.e., unique, valid, single-end, aligned read) is assigned for every record.

rname

character vector of chromosome (reference) names. When default (NULL), "chrS" is assigned for every record.

pos

integer vector of 1-based leftmost coordinates of the queries. When default (NULL), 1 is assigned for every record.

mapq

integer vector of mapping qualities. When default (NULL), 60 is assigned for every record.

cigar

character vector of CIGAR strings. When default (NULL), "lM" is assigned for every record, where `l` is the length of the query (`seq`).

rnext

character vector of chromosome (reference) names for next read in template. When default (NULL), "chrS" is assigned for every record.

pnext

integer vector of 1-based leftmost coordinates of next read in template. When default (NULL), 1 is assigned for every record.

tlen

integer vector of observed template lengths. When default (NULL), the length of the corresponding query (`seq`) is assigned for every record.

seq

character vector of query sequences. When default (NULL), random sequence is assigned. The lengths of these random sequences equal to the lengths of methylation call strings from the `XM` optional parameter (if supplied), or to the `tlen` parameter (if defined). If none of these parameters is supplied, length of every `seq` will equal 10.

qual

query sequence quality strings (ASCII of base QUALity plus 33). When default (NULL), quality of every base is assigned to "F" (QUALity of 47 + 33). The lengths of these quality strings equal to the length of the corresponding query sequences (`seq`) for every record.

...

optional tags to add to the records, in the form `tag=value`. Value can be either:

  • an integer vector to create a tag with a single integer value per alignment record (e.g., "NM" tag),

  • or a float vector to create a tag with a single float value per alignment record,

  • or a character vector (e.g., "XM" tag for methylation call string, "XG"/"YD"/"ZS" tag for reference strand read was aligned to)

  • or a list of numeric vectors to create tags array holding arrays of numeric values.

verbose

boolean to report progress and timings (default: TRUE).

Value

number of BAM records written (if `output.bam.file` is not NULL) or data.table object containing final records prepared for writing. NB: this object has 0-based coordinates and numerically encoded reference names.

Details

The function creates sample alignment records and saves them in BAM file. Output can be used to test epialleleR methods as well as other tools for methylation analysis. This method can significantly simplify calculation of methylation metrics on example data (beta, VEF, and lMHL values of epialleleR; methylation heterogeneity metrics of other tools).

The number of records written will be equal to the largest length of any supplied (nondefault) parameter or 1 if no parameters were supplied. If lengths of supplied parameters differ, shorter vectors will be recycled (a whole number of times or with remainder if necessary).

Please note that function performs almost no validity checks for supplied fields. In particular, be extra careful constructing paired-end BAM alignments, and if necessary use `samtools` to perform validity check or manual editing after BAM->SAM conversion.

See also

generateCytosineReport and generateMhlReport for methylation reports at the level of individual cytosines, as well as `epialleleR` vignettes for the description of usage and sample data.

Samtools for viewing BAM files. SAMv1 file format specifications. Specifications of optional SAM tags. metheor for ultrafast DNA methylation heterogeneity calculation from bisulfite alignments.

Examples

  out.bam <- tempfile(pattern="simulated", fileext=".bam")
  simulateBam(
    output.bam.file=out.bam,
    pos=c(1, 2),
    XM=c("ZZZzzZZZ", "ZZzzzzZZ"),
    XG=c("CT", "AG"),
    xi=5:6,
    xf=0.05,
    ai=list(as.integer(c(1:3)), as.integer(c(4:6))),
    af=list(seq(-1, 1, 0.5))
  )
#> Writing sample BAM 
#> [0.003s]
#> [1] 2
  generateCytosineReport(out.bam, threshold.reads=FALSE)
#> Checking BAM file: 
#> short-read, single-end, unsorted alignment detected
#> Reading single-end BAM file 
#> [0.002s]
#> Preparing cytosine report 
#> [0.001s]
#>      rname strand   pos context  meth unmeth
#>     <fctr> <fctr> <int>  <fctr> <int>  <int>
#>  1:   chrS      +     1      CG     1      0
#>  2:   chrS      +     2      CG     1      0
#>  3:   chrS      -     2      CG     1      0
#>  4:   chrS      +     3      CG     1      0
#>  5:   chrS      -     3      CG     1      0
#>  6:   chrS      +     4      CG     0      1
#>  7:   chrS      -     4      CG     0      1
#>  8:   chrS      +     5      CG     0      1
#>  9:   chrS      -     5      CG     0      1
#> 10:   chrS      +     6      CG     1      0
#> 11:   chrS      -     6      CG     0      1
#> 12:   chrS      +     7      CG     1      0
#> 13:   chrS      -     7      CG     0      1
#> 14:   chrS      +     8      CG     1      0
#> 15:   chrS      -     8      CG     1      0
#> 16:   chrS      -     9      CG     1      0
  # check this BAM with `samtools view` or using `output.bam.file=NULL`