predictd | R Documentation |
Predict d or fragment size from alignment results. In case of PE data, report the average insertion/fragment size from all pairs. Will NOT filter duplicates
predictd(
ifile,
gsize = "hs",
format = "AUTO",
plot = normalizePath(tempdir(), "predictd_mode.pdf"),
tsize = NULL,
bw = 300,
d_min = 20,
mfold = c(5, 50),
buffer_size = 1e+05,
verbose = 2L,
log = TRUE
)
ifile |
Input file(s). |
gsize |
Effective genome size. It can be 1.0e+9 or 1000000000, or shortcuts:'hs' for human (2.7e9), 'mm' for mouse (1.87e9), 'ce' for C. elegans (9e7) and 'dm' for fruitfly (1.2e8), Default:hs. |
format |
Input file format. |
plot |
PDF path of peak model and correlation plots. |
tsize |
Tag size. This will override the auto detected tag size. |
bw |
Band width for picking regions to compute fragment size. This value is only used while building the shifting model. DEFAULT: 300 |
d_min |
Minimum fragment size in basepair. Any predicted fragment size less than this will be excluded. DEFAULT: 20 |
mfold |
Select the regions within MFOLD range of high-confidence enrichment ratio against background to build model. Fold-enrichment in regions must be lower than upper limit, and higher than the lower limit. Use as "-m 10 30". DEFAULT:5 50 |
buffer_size |
Buffer size for incrementally increasing internal array size to store reads alignment information. DEFAULT: 100000. |
verbose |
Set verbose level of runtime message. 0: only show critical message, 1: show additional warning message, 2: show process information, 3: show debug messages. DEFAULT:2 |
log |
Whether to capture log. |
predicted fragment sizes.
eh <- ExperimentHub::ExperimentHub()
CHIP <- eh[["EH4558"]]
predictd(CHIP, d_min = 10, gsize=5.2e+7, plot = NULL)
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