Read in basic statistics about an sff file

Description

readSffGeometry processes a sff file or set of sff files, counting the number of reads and the length of each read.

Usage

readSffGeometry(filenames)

Arguments

Value

A list with two elements, nReads and Read_Widths

Author(s)

Matt Settles <msettles@uidaho.edu>

Examples

sffgeom <- readSffGeometry(system.file("extdata","Small454Test.sff",package="rSFFreader"))
sffgeom$nReads
sffgeom$Read_Widths

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(rSFFreader)
Loading required package: ShortRead
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: BiocParallel
Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/rSFFreader/readsffgeometry.Rd_%03d_medium.png", width=480, height=480)
> ### Name: readSffGeometry
> ### Title: Read in basic statistics about an sff file
> ### Aliases: readSffGeometry
> 
> ### ** Examples
> 
> sffgeom <- readSffGeometry(system.file("extdata","Small454Test.sff",package="rSFFreader"))
> sffgeom$nReads
[1] 1000
> sffgeom$Read_Widths
   [1]  938 1048 1418 1471 1026 1019  622 1414 1242  469  755  635  792 1223
  [15]  796 1058 1380 1035 1198 1229 1130  278 1248 1302  636 1035  611  953
  [29]  684 1318  902  898 1269  927  976 1400  668  664 1258 1059 1088  541
  [43] 1226  876 1077 1600  781 1048  348  782 1286 1148 1049  754 1103 1090
  [57]  663 1325  950 1166  815  951  661 1239  607 1395  721 1090 1064  796
  [71] 1117 1214 1184 1356 1384 1023  811 1182 1048 1144 1600 1599  792  848
  [85]  391  738  653  965  724  887  818 1177 1035 1354  565 1160  925 1134
  [99] 1599 1434  926 1405 1354  662  725  197  707  716  861 1354  950 1126
 [113]  477  853 1052 1597 1031  985 1024  254  366 1147  642 1138  728  716
 [127]  847 1187 1135 1148 1598 1068 1007  831 1347  737  626  862  736  762
 [141]  272  891 1171 1345 1297  571  762 1221  951  921 1118  509  799 1163
 [155]  719 1600 1339  984  897 1017 1148  983 1033 1143  806  708 1265 1172
 [169]  882 1148 1017 1185  851  930  347  663  568 1396  961  730  840 1136
 [183]  265  521 1377  985 1217  576  822 1019  626 1459 1497  846 1122  715
 [197] 1524  774 1095  472  946  862 1051  873 1203 1277 1063 1024 1225  873
 [211] 1057  742  698 1396  963 1157 1219 1300  705  757 1600  943 1438  960
 [225]  379 1425  631 1121 1234 1264  885  968 1208  871 1135  953 1281  893
 [239]  734 1019 1035 1198  684 1103 1254 1242  475  808  904  657  948 1204
 [253]  617  852 1161 1315 1023 1215 1079 1126 1192 1224  958 1173  725 1272
 [267] 1084  755  786  760 1127 1121 1111 1317 1025  520 1146 1247 1151  558
 [281] 1369 1489  648 1241 1147 1057 1102  709  735  846 1005  891 1107 1190
 [295]  554  763  839 1148 1248 1497 1031 1243 1102  638  720  679 1112  956
 [309] 1526 1134 1050  946 1600  961 1341  975  772 1109  805  546 1216  852
 [323] 1163  638  738 1213  992 1111 1118  681  907 1113  785  927 1178 1269
 [337] 1099 1107  888 1258  585 1152 1087  868  592  940 1069 1071  714 1550
 [351] 1507  789  455 1062  869  795  548  914  818 1179  774  953 1099 1134
 [365]  903 1283 1067 1362  592 1114  621  654 1208 1246 1233 1114  398  962
 [379]  593  783  837 1256  829  873 1141  968 1184  589  824 1212 1019  460
 [393]  818  848 1425  754  592 1012 1374 1181  775  791  921  918  231  900
 [407]  926 1255 1288  926  588  973 1131 1130  623 1600 1234 1261 1154  737
 [421]  962  985  901 1240  786  834 1181  991  845 1128 1284 1190  889  959
 [435]  771  973 1594  530 1501 1129  915 1160  645  280 1171 1403  867 1072
 [449]  651 1429  826  917 1280 1198  437  762  737 1102 1090 1318 1120 1053
 [463] 1291  735 1168  750 1531  606  797  986 1249 1365  771  844  872 1090
 [477]  851  797  763  912  795  867  334 1167 1266  905  313  841  429 1563
 [491]  672  347 1058  949  503  900 1053 1131  784  833  731  592  934 1091
 [505]  764 1471  621 1052  664 1278 1111 1022  923 1148 1443 1118  765  581
 [519] 1178 1170 1084  578 1599  756 1192 1150 1235  390 1130 1232 1357 1364
 [533]  819 1061  987 1423  921 1202 1109  847 1095  938 1033  954 1280  973
 [547] 1297 1070 1087  725 1120 1298  861 1041  925  657 1340  792  931 1258
 [561]  855 1403 1112  906  953 1600  919 1099  895  853 1125  774 1157 1570
 [575]  616 1055 1153  597 1248  537  707  892 1109 1143  543  732 1556 1391
 [589] 1138 1269  910 1267 1118 1151 1053 1222 1165 1597 1128  736 1354 1232
 [603] 1415 1250  947 1288 1072 1383  706  981 1162 1201  590  848  918  708
 [617] 1204  825 1120 1107 1089 1076  933  848  732 1597 1098  968 1160 1560
 [631] 1111 1099 1497 1104 1208  766  711 1081  583 1241  574  913  728  749
 [645] 1069 1362 1191 1064 1044  865  837 1250  739 1174  652  946  461 1101
 [659]  865 1045  936 1009 1130 1142  815  618  799  613 1074  653 1163  693
 [673]  760  651  532 1045 1512 1117 1045  934 1169 1132  785  918 1234 1182
 [687]  762 1026  928 1116 1118  815 1042 1252 1265  851  837  663 1346 1096
 [701]  929 1321  434 1499 1504  737  889  802  846  605 1278  807 1091 1110
 [715]  394 1035 1407 1106  977  706  884  819  359  864  825 1090  800 1124
 [729]  768  836  745  775 1126  966  385 1280 1230  878  798 1049  765 1037
 [743] 1201  964  707  943  687 1077  700  732 1071 1077  677 1144 1221 1047
 [757] 1190 1599 1313 1249 1355  673 1493  969  736  762  704 1065 1166 1212
 [771]  828  600 1155 1205  819  527  783  900 1132 1274  945 1090 1020 1226
 [785]  380  655  958 1055  677  231  775  682  939  693  897  411 1252  714
 [799]  936 1000 1508  968 1412 1443 1140 1137 1095 1215 1008  826  844  662
 [813]  499  893  862  673 1457 1100  932  910 1152 1013 1266 1102 1050 1057
 [827] 1094 1466 1082 1289 1143  755 1211  430  724 1204 1418  877 1120 1032
 [841]  664  691 1202 1004  932  798 1065  838  927  646  772 1229 1383 1098
 [855] 1227  962  989 1161 1439 1083  811 1040  947  859  671  654 1018 1439
 [869] 1090 1047  729  550 1007  963  939 1189 1068  781 1085  951  885 1381
 [883] 1233 1097 1096  948  711 1318  968 1085  706  995  922 1242  989  722
 [897]  661  909 1043 1157 1599  714  921  776  472  779 1194  833  789  994
 [911] 1342  967  695  552  772 1056  734 1064 1138 1228  927 1280  660  867
 [925] 1356 1029  899 1302  792 1108 1223 1100  948 1200 1052  815 1296  896
 [939]  908 1087 1246  752 1201  797 1088 1030  645 1289 1243  747  319  930
 [953]  575 1120  787 1183  762 1048 1119 1039  704  953 1044 1128 1109 1213
 [967] 1419  789  878 1198 1065 1131 1216 1270  636 1208 1377 1148 1228  780
 [981]  809  621 1125 1135 1048 1175  941 1332  934 1059  646  747 1171  474
 [995]  290 1272  987 1411  950 1316
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>