Description Usage Arguments Details Author(s) Examples

GWplot function plots -log_10 p-value based on SNP's chromosomal position in bitmap format.

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`data` |
a dataframe that contains p-values, chromosome number and physical position of SNPs |

`pval` |
a character string correspong to the name of the p-value column |

`pos` |
a character string correspong to the name of column with SNP physical positions |

`chr` |
a character string correspong to the name of column with SNP chromosome number |

`chr.plot` |
the chsomosomes of interest for GWplot; either 1:22 or c(1:22,"X"), default chr.plot=c(1:22,"X"), "X" for X chromosome |

`title.text` |
the title of the genome-wide p-value plot |

`ylim` |
the maximum of -log_10 p-value to be plotted, useful when not want to plot extremely small p-values |

`outfile` |
the file name (xxxx.bmp) for output plot in bitmap format |

`cutoff1` |
genome-wide significance; default is 5E-8 ; p-values below this threshold will be highlighted in red |

`cutoff2` |
suggestive genome-wide significance; default is 4E-7; p-values below this threshold but above cutoff1 will be highlighted in blue |

When the dataset has 0 p-value, GWplot will generate pvalzero.csv that contain the results with 0 p-value and make the genome-wide p-value plot by replacing 0 p-value with 5E-324. P-values that reach genome-wide significance are displayed in red color; P-values that reach suggestive genome-wide significance but not genome-wide significance are displayed in blue color.

Qiong Yang <qyang@bu.edu> and Ming-Huei Chen <mhchen@bu.edu>

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