Collapse full coverage information for efficient quantile computations

Source: R/collapseFullCoverage.R

For a given data set this function collapses the full coverage information for each sample from all the chromosomes. The resulting information per sample is the number of bases with coverage 0, 1, etc. It is similar to using table() on a regular vector. This information is then used by sampleDepth for calculating the sample depth adjustments. The data set can loaded to R using (see fullCoverage) and optionally filtered using filterData.

collapseFullCoverage(fullCov, colsubset = NULL, save = FALSE, ...)

Arguments

fullCov

A list where each element is the result from loadCoverage used with cutoff=NULL. Can be generated using fullCoverage.

colsubset

Which columns of coverageInfo$coverage to use.

save

If TRUE, the result is saved as 'collapsedFull.Rdata'.

...

Arguments passed to other methods and/or advanced arguments. Advanced arguments:

verbose

If TRUE basic status updates will be printed along the way. Default: FALSE.

Value

A list with one element per sample. Then per sample, a list with two vector elements: values and weights. The first one is the coverage value and the second one is the number of bases with that value.

Author

Leonardo Collado-Torres

Examples

## Collapse the coverage information for the filtered data
collapsedFull <- collapseFullCoverage(list(genomeData),
    verbose = TRUE
)
#> 2023-05-07 06:01:10.425638 collapseFullCoverage: Sorting fullCov
#> 2023-05-07 06:01:10.428074 collapseFullCoverage: Collapsing chromosomes information by sample
collapsedFull
#> $ERR009101
#> $ERR009101$values
#> [1] 0 1 2
#> 
#> $ERR009101$weights
#> [1] 1105  298   31
#> 
#> 
#> $ERR009102
#> $ERR009102$values
#> [1] 0 1 2
#> 
#> $ERR009102$weights
#> [1] 1216  216    2
#> 
#> 
#> $ERR009105
#> $ERR009105$values
#> [1] 0 1 2 3 4 5 6 7
#> 
#> $ERR009105$weights
#> [1] 726 226 204  67  52  93  38  28
#> 
#> 
#> $ERR009107
#> $ERR009107$values
#> [1] 0 1 2 3 4 5 6
#> 
#> $ERR009107$weights
#> [1] 1156  125  115    2    3   17   16
#> 
#> 
#> $ERR009108
#> $ERR009108$values
#> [1] 0 1 2 3
#> 
#> $ERR009108$weights
#> [1] 1193   74  131   36
#> 
#> 
#> $ERR009112
#> $ERR009112$values
#> [1] 0 1 2
#> 
#> $ERR009112$weights
#> [1] 1161  258   15
#> 
#> 
#> $ERR009115
#> $ERR009115$values
#> [1] 0 1
#> 
#> $ERR009115$weights
#> [1] 1396   38
#> 
#> 
#> $ERR009116
#> $ERR009116$values
#> [1] 0 1 2
#> 
#> $ERR009116$weights
#> [1] 1120  269   45
#> 
#> 
#> $ERR009131
#> $ERR009131$values
#> [1] 0 1 2
#> 
#> $ERR009131$weights
#> [1] 1299  122   13
#> 
#> 
#> $ERR009138
#> $ERR009138$values
#> [1] 0 1 2 3
#> 
#> $ERR009138$weights
#> [1] 1089  306   25   14
#> 
#> 
#> $ERR009144
#> $ERR009144$values
#> [1] 0 1 2
#> 
#> $ERR009144$weights
#> [1] 1097  232  105
#> 
#> 
#> $ERR009145
#> $ERR009145$values
#> [1] 0 1
#> 
#> $ERR009145$weights
#> [1] 1360   74
#> 
#> 
#> $ERR009148
#> $ERR009148$values
#> [1] 0 1 2 3
#> 
#> $ERR009148$weights
#> [1] 1212  133   76   13
#> 
#> 
#> $ERR009151
#> $ERR009151$values
#> [1] 0 1 2 3 4 5
#> 
#> $ERR009151$weights
#> [1] 972 186 172  62  38   4
#> 
#> 
#> $ERR009152
#> $ERR009152$values
#> [1] 0 1 2
#> 
#> $ERR009152$weights
#> [1] 1059  232  143
#> 
#> 
#> $ERR009153
#> $ERR009153$values
#> [1] 0 1 2 3 4
#> 
#> $ERR009153$weights
#> [1] 1104  275   45    9    1
#> 
#> 
#> $ERR009159
#> $ERR009159$values
#> [1] 0 1 2 3 4 5
#> 
#> $ERR009159$weights
#> [1] 975 169 154  63  69   4
#> 
#> 
#> $ERR009161
#> $ERR009161$values
#> [1] 0 1 2 3 4
#> 
#> $ERR009161$weights
#> [1] 1243   96   61   30    4
#> 
#> 
#> $ERR009163
#> $ERR009163$values
#> [1] 0 1
#> 
#> $ERR009163$weights
#> [1] 1360   74
#> 
#> 
#> $ERR009164
#> $ERR009164$values
#> [1] 0 1 2 3
#> 
#> $ERR009164$weights
#> [1] 1336   32   46   20
#> 
#> 
#> $ERR009167
#> $ERR009167$values
#>  [1] 0 1 2 3 4 5 6 7 8 9
#> 
#> $ERR009167$weights
#>  [1] 728 200 181 140  79  17  25  23  24  17
#> 
#> 
#> $SRR031812
#> $SRR031812$values
#> [1] 0 1
#> 
#> $SRR031812$weights
#> [1] 1399   35
#> 
#> 
#> $SRR031835
#> $SRR031835$values
#> [1] 0 1
#> 
#> $SRR031835$weights
#> [1] 1388   46
#> 
#> 
#> $SRR031867
#> $SRR031867$values
#> [1] 0
#> 
#> $SRR031867$weights
#> [1] 1434
#> 
#> 
#> $SRR031868
#> $SRR031868$values
#> [1] 0
#> 
#> $SRR031868$weights
#> [1] 1434
#> 
#> 
#> $SRR031900
#> $SRR031900$values
#> [1] 0
#> 
#> $SRR031900$weights
#> [1] 1434
#> 
#> 
#> $SRR031904
#> $SRR031904$values
#> [1] 0 1
#> 
#> $SRR031904$weights
#> [1] 1388   46
#> 
#> 
#> $SRR031914
#> $SRR031914$values
#> [1] 0
#> 
#> $SRR031914$weights
#> [1] 1434
#> 
#> 
#> $SRR031936
#> $SRR031936$values
#> [1] 0
#> 
#> $SRR031936$weights
#> [1] 1434
#> 
#> 
#> $SRR031958
#> $SRR031958$values
#> [1] 0
#> 
#> $SRR031958$weights
#> [1] 1434
#> 
#> 
#> $SRR031960
#> $SRR031960$values
#> [1] 0
#> 
#> $SRR031960$weights
#> [1] 1434
#> 
#> 
if (FALSE) {
## You can also collapsed the raw data
collapsedFullRaw <- collapseFullCoverage(list(genomeDataRaw), verbose = TRUE)
}