Description Usage Arguments Value Author(s) References See Also Examples

Performs smooth-log2-ratio calculation given control and treated GRanges generated by comp() function.

1 2 | ```
slograt(control_GR, treated_GR, window_size = 5, nt_offset = 1,
depth_correction = "all", pseudocount = 5, add_to)
``` |

`control_GR` |
GRanges object made by comp() function from the control sample. |

`treated_GR` |
GRanges object made by comp() function from the treated sample. |

`window_size` |
if smoothing is to be performed, then what should be the window size? (use only odd numbers to ensure that windows are centred on a nucleotide of interest) (default: 5) |

`nt_offset` |
How many position in the 5' direction should the signal be offset to account for the fact that reverse transcription termination occurs before site of modification. |

`depth_correction` |
One of three values: "no" - counts are used as given, "all" - counts from sample with higher total sum of EUCs are multiplied by sum of EUCs from sample with lower total sum of EUCs and divided by sum of EUCs from sample with higher EUC count (default), "RNA" as in "all" but on per RNA basis |

`pseudocount` |
What pseudocount should be added to each nucleotide prior to calculating log2 ratio (default: 5) |

`add_to` |
GRanges object made by other normalization function (dtcr(), slograt(), swinsor(), compdata()) to which normalized values should be added. |

GRanges object with "slograt" (smooth log2 ratio) and "slograt.p" (p.value of comparing control and treated) metadata.

Lukasz Jan Kielpinski, Nikos Sidiropoulos

Wan, Y., Qu, K., Zhang, Q.C., Flynn, R.A., Manor, O., Ouyang, Z., Zhang, J., Spitale, R.C., Snyder, M.P., Segal, E., et al. (2014). Landscape and variation of RNA secondary structure across the human transcriptome. Nature 505, 706-709.

`comp`

, `dtcr`

, `compdata`

,
`swinsor`

, `GR2norm_df`

, `plotRNA`

,
`norm2bedgraph`

1 2 3 4 5 6 7 8 9 10 11 | ```
dummy_euc_GR_control <- GRanges(seqnames="DummyRNA",
IRanges(start=round(runif(100)*100),
width=round(runif(100)*100+1)), strand="+",
EUC=round(runif(100)*100))
dummy_euc_GR_treated <- GRanges(seqnames="DummyRNA",
IRanges(start=round(runif(100)*100),
width=round(runif(100)*100+1)), strand="+",
EUC=round(runif(100)*100))
dummy_comp_GR_control <- comp(dummy_euc_GR_control)
dummy_comp_GR_treated <- comp(dummy_euc_GR_treated)
slograt(control_GR=dummy_comp_GR_control, treated_GR=dummy_comp_GR_treated)
``` |

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