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2
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1 Changes in version 1.5.4:
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2
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3 o Polish help documents of constructBins(), generateWig(), and mosaicsRunAll().
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4
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5 o Polish the vignette.
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6
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7 Changes in version 1.5.3:
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8
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9 BUG FIXES
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10
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11 o mosaicsRunAll(): Bug fix when byChr = TRUE.
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12
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13 Changes in version 1.5.2:
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14
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15 SIGNIFICANT USER-VISIBLE CHANGES
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16
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17 o constructBins(): Supports aligned read file formats for PET data (eland results and SAM formats).
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18
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19 o mosaicsRunAll(): Supports aligned read file formats for PET data.
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20
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21 o Add generateWig(): Constructs wiggle files for PET and SET data.
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22
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23 o Use tab separator instead of whitespaces for generateWig() and constructBins().
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24
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25 o Improve the vignette (case studies, example lines for input files, generateWig()).
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26
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27 BUG FIXES
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28
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29 o constructBins(): Bug fix for capping and excludeChr. Fix incorrect summary when byChr = TRUE.
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30
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31 o mosaicsRunAll(): Bug fix for excludeChr & handling the full path for chipFile and controlFile.
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32
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33 Changes in version 1.5.1:
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34
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35 SIGNIFICANT USER-VISIBLE CHANGES
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36
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37 o constructBins(): Chromosome information can now be specified.
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38
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39 o mosaicsRunAll(): Chromosome information can now be specified.
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40
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41
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42 Changes in version 1.4.1:
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43
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44 BUG FIXES
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45
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46 o constructBins(): Bug fix for the "outfileLoc" argument.
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47
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48 o mosaicsFit(): Minor changes in two-signal-component model fitting.
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49
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50 o mosaicsPeak(): No warning with the updated IRanges package.
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51
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52
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53 Changes in version 1.3.4:
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54
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55 SIGNIFICANT USER-VISIBLE CHANGES
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56
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57 o Improve help documents for all classes and functions.
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58
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59 BUG FIXES
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60
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61 o mosaicsPeak(): Correct bin size calculation when binsize=NA.
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62
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63 Changes in version 1.3.2:
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64
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65 SIGNIFICANT USER-VISIBLE CHANGES
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66
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67 o Simplify arguments of mosaicsRunAll(), constructBind(), and export().
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68
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69 o Add parallel argument in mosaicsFit().
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70
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71 o Extensive use of parallel processing/computing.
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72
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73 o Overall speed improvements in the package.
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74
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75 o Update the vignette.
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76
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77 o Use parallel package instead of multicore package.
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78
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79 Changes in version 1.2.5:
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80
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81 o Correct version number in DESCRIPTION and package?mosaics.
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82
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83 Changes in version 1.2.4:
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84
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85 SIGNIFICANT USER-VISIBLE CHANGES
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86
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87 o Add parallel argument in readBins().
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88
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89 o Add parallel argument in mosaicsRunAll().
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90
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91 BUG FIXES
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92
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93 o DESCRIPTION: 'multicore' package in 'Enhances' instead of 'Suggests'.
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94
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95 Changes in version 1.2.3:
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96
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97 NEW FEATURES
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98
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99 o New model for deeply sequenced ChIP-seq data.
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100
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101 o Genome-wide analysis of ChIP-seq data is now available.
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102
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103 o Supports more aligned read file formats: eland_result, eland_extended, eland_export, bowtie, SAM, BED, CSEM.
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104
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105 o Preprocessing of aligned read files can be done within the R environment using constructBins().
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106
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107 o Easier model fitting for the two sample analysis using mosaicsRunAll().
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108
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109 o Preprocessing and model fitting become much faster (Rcpp).
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110
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111 o Parallel processing/computing is now supported (multicore).
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112
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113 SIGNIFICANT USER-VISIBLE CHANGES
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114
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115 o Add constructBins(): Preprocess aligned read files to bin-level files.
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116
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117 o Add mosaicsRunAll(): Convenient two sample analysis.
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118
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119 o Add bgEst argument in mosaicsFit(): Choose background estimation approach.
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120
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121 o Add nCore argument in readBins(): Parallel processing.
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122
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123 o Vignettes is now extensively updated.
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124
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125 o Rcpp package is required and multicore package is suggested.
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126
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127 DEPRECATED AND DEFUNCT
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128
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129 o Drop chrID argument in export().
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130
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131 BUG FIXES
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132
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133 o Fix mosaicsPeak() for the case that no peak is called.
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134
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135 o Fix export() by removing unnecessary spaces in output text files.
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136
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137 Changes in version 1.2.0:
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138
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139 o BioConductor release 2.9.
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140
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141 Changes in version 1.0.1:
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142
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143 o Fixes for 'plot' method of class 'binData'.
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144
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145 Changes in version 1.0.0:
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146
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147 o On BioConductor (release 2.8).
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